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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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Keller J, Diggs LP, Hsueh EC. Prognostic molecular testing in melanoma: ready for prime time? Melanoma Manag 2017; 4:171-174. [PMID: 30190922 DOI: 10.2217/mmt-2017-0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/16/2017] [Indexed: 01/02/2023] Open
Affiliation(s)
- Jennifer Keller
- Department of Surgery, Saint Louis University, St Louis, MO, USA
| | - Laurence P Diggs
- Department of Surgery, Saint Louis University, St Louis, MO, USA
| | - Eddy C Hsueh
- Department of Surgery, Saint Louis University, St Louis, MO, USA
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103
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Eskiocak B, McMillan EA, Mendiratta S, Kollipara RK, Zhang H, Humphries CG, Wang C, Garcia-Rodriguez J, Ding M, Zaman A, Rosales TI, Eskiocak U, Smith MP, Sudderth J, Komurov K, Deberardinis RJ, Wellbrock C, Davies MA, Wargo JA, Yu Y, De Brabander JK, Williams NS, Chin L, Rizos H, Long GV, Kittler R, White MA. Biomarker Accessible and Chemically Addressable Mechanistic Subtypes of BRAF Melanoma. Cancer Discov 2017; 7:832-851. [PMID: 28455392 DOI: 10.1158/2159-8290.cd-16-0955] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/07/2016] [Accepted: 04/26/2017] [Indexed: 12/21/2022]
Abstract
Genomic diversity among melanoma tumors limits durable control with conventional and targeted therapies. Nevertheless, pathologic activation of the ERK1/2 pathway is a linchpin tumorigenic mechanism associated with the majority of primary and recurrent disease. Therefore, we sought to identify therapeutic targets that are selectively required for tumorigenicity in the presence of pathologic ERK1/2 signaling. By integration of multigenome chemical and genetic screens, recurrent architectural variants in melanoma tumor genomes, and patient outcome data, we identified two mechanistic subtypes of BRAFV600 melanoma that inform new cancer cell biology and offer new therapeutic opportunities. Subtype membership defines sensitivity to clinical MEK inhibitors versus TBK1/IKBKε inhibitors. Importantly, subtype membership can be predicted using a robust quantitative five-feature genetic biomarker. This biomarker, and the mechanistic relationships linked to it, can identify a cohort of best responders to clinical MEK inhibitors and identify a cohort of TBK1/IKBKε inhibitor-sensitive disease among nonresponders to current targeted therapy.Significance: This study identified two mechanistic subtypes of melanoma: (1) the best responders to clinical BRAF/MEK inhibitors (25%) and (2) nonresponders due to primary resistance mechanisms (9.9%). We identified robust biomarkers that can detect these subtypes in patient samples and predict clinical outcome. TBK1/IKBKε inhibitors were selectively toxic to drug-resistant melanoma. Cancer Discov; 7(8); 832-51. ©2017 AACR.See related commentary by Jenkins and Barbie, p. 799This article is highlighted in the In This Issue feature, p. 783.
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Affiliation(s)
- Banu Eskiocak
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Elizabeth A McMillan
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Saurabh Mendiratta
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hailei Zhang
- The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Caroline G Humphries
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Changguang Wang
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jose Garcia-Rodriguez
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ming Ding
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Aubhishek Zaman
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Tracy I Rosales
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ugur Eskiocak
- Children's Research Institute and the Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Michael P Smith
- Manchester Cancer Research Centre, Wellcome Trust Centre for Cell-Matrix Research, The University of Manchester, Manchester, United Kingdom
| | - Jessica Sudderth
- Children's Research Institute and the Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kakajan Komurov
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Ralph J Deberardinis
- Children's Research Institute and the Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Claudia Wellbrock
- Manchester Cancer Research Centre, Wellcome Trust Centre for Cell-Matrix Research, The University of Manchester, Manchester, United Kingdom
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yonghao Yu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jef K De Brabander
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Noelle S Williams
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lynda Chin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Helen Rizos
- Melanoma Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Ralf Kittler
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Michael A White
- Department of Cell Biology, The University of Texas Southwestern Medical Center, Dallas, Texas.
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Welinder C, Pawłowski K, Szasz AM, Yakovleva M, Sugihara Y, Malm J, Jönsson G, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Laurell T, Wieslander E, Marko-Varga G. Correlation of histopathologic characteristics to protein expression and function in malignant melanoma. PLoS One 2017; 12:e0176167. [PMID: 28445515 PMCID: PMC5405986 DOI: 10.1371/journal.pone.0176167] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 04/06/2017] [Indexed: 12/11/2022] Open
Abstract
Background Metastatic melanoma is still one of the most prevalent skin cancers, which upon progression has neither a prognostic marker nor a specific and lasting treatment. Proteomic analysis is a versatile approach with high throughput data and results that can be used for characterizing tissue samples. However, such analysis is hampered by the complexity of the disease, heterogeneity of patients, tumors, and samples themselves. With the long term aim of quest for better diagnostics biomarkers, as well as predictive and prognostic markers, we focused on relating high resolution proteomics data to careful histopathological evaluation of the tumor samples and patient survival information. Patients and methods Regional lymph node metastases obtained from ten patients with metastatic melanoma (stage III) were analyzed by histopathology and proteomics using mass spectrometry. Out of the ten patients, six had clinical follow-up data. The protein deep mining mass spectrometry data was related to the histopathology tumor tissue sections adjacent to the area used for deep-mining. Clinical follow-up data provided information on disease progression which could be linked to protein expression aiming to identify tissue-based specific protein markers for metastatic melanoma and prognostic factors for prediction of progression of stage III disease. Results In this feasibility study, several proteins were identified that positively correlated to tumor tissue content including IF6, ARF4, MUC18, UBC12, CSPG4, PCNA, PMEL and MAGD2. The study also identified MYC, HNF4A and TGFB1 as top upstream regulators correlating to tumor tissue content. Other proteins were inversely correlated to tumor tissue content, the most significant being; TENX, EHD2, ZA2G, AOC3, FETUA and THRB. A number of proteins were significantly related to clinical outcome, among these, HEXB, PKM and GPNMB stood out, as hallmarks of processes involved in progression from stage III to stage IV disease and poor survival. Conclusion In this feasibility study, promising results show the feasibility of relating proteomics to histopathology and clinical outcome, and insight thus can be gained into the molecular processes driving the disease. The combined analysis of histological features including the sample cellular composition with protein expression of each metastasis enabled the identification of novel, differentially expressed proteins. Further studies are necessary to determine whether these putative biomarkers can be utilized in diagnostics and prognostic prediction of metastatic melanoma.
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Affiliation(s)
- Charlotte Welinder
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Krzysztof Pawłowski
- Faculty of Agriculture and Biology, Dept. of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Warszawa, Poland
- Dept. of Translational Medicine, Lund University, Malmö, Sweden
| | - A. Marcell Szasz
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- 2nd Dept. of Pathology, Semmelweis University, Budapest, Hungary
| | - Maria Yakovleva
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
| | - Yutaka Sugihara
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Malm
- Centre of Excellence in Biological and Medical Mass Spectrometry “CEBMMS”, Biomedical Centre D13, Lund University, Lund, Sweden
- Dept. of Translational Medicine, Lund University, Malmö, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Christian Ingvar
- Dept. of Surgery, Dept. of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Dept. of Oncology, Skåne University Hospital, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
- Dept. of Oncology, 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, BMC D13, 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, BMC D13, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Dept. of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - 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, BMC D13, Lund, Sweden
- First Dept. of Surgery, Tokyo Medical University, Tokyo, Japan
- * E-mail:
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105
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Cirenajwis H, Lauss M, Ekedahl H, Törngren T, Kvist A, Saal LH, Olsson H, Staaf J, Carneiro A, Ingvar C, Harbst K, Hayward NK, Jönsson G. NF1-mutated melanoma tumors harbor distinct clinical and biological characteristics. Mol Oncol 2017; 11:438-451. [PMID: 28267273 PMCID: PMC5527484 DOI: 10.1002/1878-0261.12050] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/14/2017] [Accepted: 02/14/2017] [Indexed: 12/30/2022] Open
Abstract
In general, melanoma can be considered as a UV‐driven disease with an aggressive metastatic course and high mutational load, with only few tumors (acral, mucosal, and uveal melanomas) not induced by sunlight and possessing a lower mutational load. The most commonly activated pathway in melanoma is the mitogen‐activated protein kinase (MAPK) pathway. However, the prognostic significance of mutational stratification is unclear and needs further investigation. Here, in silico we combined mutation data from 162 melanomas subjected to targeted deep sequencing with mutation data from three published studies. Tumors from 870 patients were grouped according to BRAF,RAS,NF1 mutation or triple‐wild‐type status and correlated with tumor and patient characteristics. We found that the NF1‐mutated subtype had a higher mutational burden and strongest UV mutation signature. Searching for co‐occurring mutated genes revealed the RASopathy genes PTPN11 and RASA2, as well as another RAS domain‐containing gene RASSF2 enriched in the NF1 subtype after adjustment for mutational burden. We found that a larger proportion of the NF1‐mutant tumors were from males and with older age at diagnosis. Importantly, we found an increased risk of death from melanoma (disease‐specific survival, DSS; HR, 1.9; 95% CI, 1.21–3.10; P = 0.046) and poor overall survival (OS; HR, 2.0; 95% CI, 1.28–2.98; P = 0.01) in the NF1 subtype, which remained significant after adjustment for age, gender, and lesion type (DSS P = 0.03, OS P = 0.06, respectively). Melanoma genomic subtypes display different biological and clinical characteristics. The poor outcome observed in the NF1 subtype highlights the need for improved characterization of this group.
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Affiliation(s)
- Helena Cirenajwis
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden
| | - Martin Lauss
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden
| | - Henrik Ekedahl
- Division of Surgery, Department of Clinical Sciences, Lund University, Sweden
| | - Therese Törngren
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden
| | - Lao H Saal
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden.,Department of Oncology, Skåne University Hospital, Lund University, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden
| | - Ana Carneiro
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden.,Department of Oncology, Skåne University Hospital, Lund University, Sweden
| | - Christian Ingvar
- Division of Surgery, Department of Clinical Sciences, Lund University, Sweden
| | - Katja Harbst
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden
| | | | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Sweden
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106
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Puig-Butille JA, Vinyals A, Ferreres JR, Aguilera P, Cabré E, Tell-Martí G, Marcoval J, Mateo F, Palomero L, Badenas C, Piulats JM, Malvehy J, Pujana MA, Puig S, Fabra À. AURKA Overexpression Is Driven by FOXM1 and MAPK/ERK Activation in Melanoma Cells Harboring BRAF or NRAS Mutations: Impact on Melanoma Prognosis and Therapy. J Invest Dermatol 2017; 137:1297-1310. [PMID: 28188776 DOI: 10.1016/j.jid.2017.01.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 01/04/2017] [Accepted: 01/16/2017] [Indexed: 12/31/2022]
Abstract
The cell cycle-related genes AURKA and FOXM1 are overexpressed in melanoma. We show here that AURKA overexpression is associated with poor prognosis in three independent cohorts of melanoma patients and correlates with the presence of genomic amplification of AURKA locus and BRAFV600E mutation. AURKA overexpression may also be driven by increased promoter activation through elements such as ETS and FOXM1 found within the 5' proximal promoter region. Activated MAPK/ERK signaling pathway mediates robust AURKA promoter activation, thereby knockdown of BRAFV600E and ERK inhibition results in reduced AURKA transcription and expression. We show a positive correlation between FOXM1 and AURKA expression in three independent cohorts of melanoma patients. FOXM1 silencing decreases expression of AURKA and late cell cycle genes in melanoma cells. We further found that FOXM1 expression levels are significantly higher in tumors carrying the BRAFV600E mutation compared with the wild-type BRAF (BRAFwt). Accordingly, the knockdown of BRAFV600E also reduces the expression of FOXM1 in BRAFV600E cells. Moreover, Aurora kinase A and FOXM1 inhibition by either genetic knockdown or pharmacologic inhibitors impair melanoma growth and survival both in culture and in vivo, underscoring their therapeutic value for melanoma patients who fail to benefit from BRAF/MEK signaling inhibition.
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Affiliation(s)
- Joan Anton Puig-Butille
- Biochemistry and Molecular Genetics Service, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Antònia Vinyals
- IDIBELL (Bellvitge Biomedical Research Institute), Centre d' Oncologia Molecular, Barcelona, Spain
| | - Josep R Ferreres
- Dermatology Service, IDIBELL-Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Paula Aguilera
- Dermatology Department, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Eduard Cabré
- IDIBELL (Bellvitge Biomedical Research Institute), Centre d' Oncologia Molecular, Barcelona, Spain
| | - Gemma Tell-Martí
- Dermatology Department, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Joaquim Marcoval
- Dermatology Service, IDIBELL-Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Francesca Mateo
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), IDIBELL, Barcelona, Spain
| | - Luís Palomero
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), IDIBELL, Barcelona, Spain
| | - Celia Badenas
- Biochemistry and Molecular Genetics Service, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Josep M Piulats
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), IDIBELL, Barcelona, Spain
| | - Josep Malvehy
- Dermatology Department, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Miquel A Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), IDIBELL, Barcelona, Spain
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Àngels Fabra
- IDIBELL (Bellvitge Biomedical Research Institute), Centre d' Oncologia Molecular, Barcelona, Spain.
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107
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Next-Generation Sequencing Reveals Pathway Activations and New Routes to Targeted Therapies in Cutaneous Metastatic Melanoma. Am J Dermatopathol 2017; 39:1-13. [PMID: 28045747 DOI: 10.1097/dad.0000000000000729] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Comprehensive genomic profiling of clinical samples by next-generation sequencing (NGS) can identify one or more therapy targets for the treatment of metastatic melanoma (MM) with a single diagnostic test. METHODS NGS was performed on hybridization-captured, adaptor ligation-based libraries using DNA extracted from 4 formalin-fixed paraffin-embedded sections cut at 10 microns from 30 MM cases. The exons of 182 cancer-related genes were fully sequenced using the Illumina HiSeq 2000 at an average sequencing depth of 1098X and evaluated for genomic alterations (GAs) including point mutations, insertions, deletions, copy number alterations, and select gene fusions/rearrangements. Clinically relevant GAs (CRGAs) were defined as those identifying commercially available targeted therapeutics or therapies in registered clinical trials. RESULTS The 30 American Joint Committee on Cancer Stage IV MM included 17 (57%) male and 13 (43%) female patients with a mean age of 59.5 years (range 41-83 years). All MM samples had at least 1 GA, and an average of 2.7 GA/sample (range 1-7) was identified. The mean number of GA did not differ based on age or sex; however, on average, significantly more GAs were identified in amelanotic and poorly differentiated MM. GAs were most commonly identified in BRAF (12 cases, 40%), CDKN2A (6 cases, 20%), NF1 (8 cases, 26.7%), and NRAS (6 cases, 20%). CRGAs were identified in all patients, and represented 77% of the GA (64/83) detected. The median and mean CRGAs per tumor were 2 and 2.1, respectively (range 1-7). CONCLUSION Comprehensive genomic profiling of MM, using a single diagnostic test, uncovers an unexpectedly high number of CRGA that would not be identified by standard of care testing. Moreover, NGS has the potential to influence therapy selection and can direct patients to enter relevant clinical trials evaluating promising targeted therapies.
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108
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Abstract
Malignant melanoma of the skin is the most aggressive human cancer given that a primary tumor a few millimeters in diameter frequently has full metastatic competence. In view of that, revealing the genetic background of this potential may also help to better understand tumor dissemination in general. Genomic analyses have established the molecular classification of melanoma based on the most frequent driver oncogenic mutations (BRAF, NRAS, KIT) and have also revealed a long list of rare events, including mutations and amplifications as well as genetic microheterogeneity. At the moment, it is unclear whether any of these rare events have role in the metastasis initiation process since the major drivers do not have such a role. During lymphatic and hematogenous dissemination, the clonal selection process is evidently reflected by differences in oncogenic drivers in the metastases versus the primary tumor. Clonal selection is also evident during lymphatic progression, though the genetic background of this immunoselection is less clear. Genomic analyses of metastases identified further genetic alterations, some of which may correspond to metastasis maintenance genes. The natural genetic progression of melanoma can be modified by targeted (BRAF or MEK inhibitor) or immunotherapies. Some of the rare events in primary tumors may result in primary resistance, while further new genetic lesions develop during the acquired resistance to both targeted and immunotherapies. Only a few genetic lesions of the primary tumor are constant during natural or therapy-modulated progression. EGFR4 and NMDAR2 mutations, MITF and MET amplifications and PTEN loss can be considered as metastasis drivers. Furthermore, BRAF and MITF amplifications as well as PTEN loss are also responsible for resistance to targeted therapies, whereas NRAS mutation is the only founder genetic lesion showing any association with sensitivity to immunotherapies. Unfortunately, there are hardly any data on the possible organ-specific metastatic drivers in melanoma. These observations suggest that clinical management of melanoma patients must rely on the genetic analysis of the metastatic lesions to be able to monitor progression-associated changes and to personalize therapies.
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109
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Lauss M, Nsengimana J, Staaf J, Newton-Bishop J, Jönsson G. Consensus of Melanoma Gene Expression Subtypes Converges on Biological Entities. J Invest Dermatol 2016; 136:2502-2505. [PMID: 27345472 DOI: 10.1016/j.jid.2016.05.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/09/2016] [Accepted: 05/31/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Martin Lauss
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, Sweden
| | - Jeremie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Johan Staaf
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, Sweden
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Göran Jönsson
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, Sweden.
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110
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Generation of metastatic melanoma specific antibodies by affinity purification. Sci Rep 2016; 6:37253. [PMID: 27853253 PMCID: PMC5112778 DOI: 10.1038/srep37253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/26/2016] [Indexed: 12/03/2022] Open
Abstract
Melanoma is the most aggressive type of skin cancer and one of the most frequent tumours in young adults. Identification of primary tumours prone to develop metastasis is of paramount importance for further patient stratification. However, till today, no markers exist that are routinely used to predict melanoma progression. To ameliorate this problem, we generated antiserum directed against metastatic melanoma tissue lysate and applied a novel approach to purify the obtained serum via consecutive affinity chromatography steps. The established antibody, termed MHA-3, showed high reactivity against metastatic melanoma cell lines both in vitro and in vivo. We also tested MHA-3 on 227 melanoma patient samples and compared staining with the melanoma marker S100b. Importantly, MHA-3 was able to differentiate between metastatic and non-metastatic melanoma samples. By proteome analysis we identified 18 distinct antigens bound by MHA-3. Combined expression profiling of all identified proteins revealed a significant survival difference in melanoma patients. In conclusion, we developed a polyclonal antibody, which is able to detect metastatic melanoma on paraffin embedded sections. Hence, we propose that this antibody will represent a valuable additional tool for precise melanoma diagnosis.
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111
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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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112
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Clancy T, Hovig E. Profiling networks of distinct immune-cells in tumors. BMC Bioinformatics 2016; 17:263. [PMID: 27377892 PMCID: PMC4932723 DOI: 10.1186/s12859-016-1141-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/20/2016] [Indexed: 11/16/2022] Open
Abstract
Background It is now clearly evident that cancer outcome and response to therapy is guided by diverse immune-cell activity in tumors. Presently, a key challenge is to comprehensively identify networks of distinct immune-cell signatures present in complex tissue, at higher-resolution and at various stages of differentiation, activation or function. This is particularly so for closely related immune-cells with diminutive, yet critical, differences. Results To predict networks of infiltrated distinct immune-cell phenotypes at higher resolution, we explored an integrated knowledge-based approach to select immune-cell signature genes integrating not only expression enrichment across immune-cells, but also an automatic capture of relevant immune-cell signature genes from the literature. This knowledge-based approach was integrated with resources of immune-cell specific protein networks, to define signature genes of distinct immune-cell phenotypes. We demonstrate the utility of this approach by profiling signatures of distinct immune-cells, and networks of immune-cells, from metastatic melanoma patients who had undergone chemotherapy. The resultant bioinformatics strategy complements immunohistochemistry from these tumors, and predicts both tumor-killing and immunosuppressive networks of distinct immune-cells in responders and non-responders, respectively. The approach is also shown to capture differences in the immune-cell networks of BRAF versus NRAS mutated metastatic melanomas, and the dynamic changes in resistance to targeted kinase inhibitors in MAPK signalling. Conclusions This integrative bioinformatics approach demonstrates that capturing the protein network signatures and ratios of distinct immune-cell in the tumor microenvironment maybe an important factor in predicting response to therapy. This may serve as a computational strategy to define network signatures of distinct immune-cells to guide immuno-pathological discovery. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1141-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Trevor Clancy
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway. .,Department of Cancer Immunology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Biomedical Research Group, Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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113
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Wicki A, Mandalà M, Massi D, Taverna D, Tang H, Hemmings BA, Xue G. Acquired Resistance to Clinical Cancer Therapy: A Twist in Physiological Signaling. Physiol Rev 2016; 96:805-29. [DOI: 10.1152/physrev.00024.2015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Although modern therapeutic strategies have brought significant progress to cancer care in the last 30 years, drug resistance to targeted monotherapies has emerged as a major challenge. Aberrant regulation of multiple physiological signaling pathways indispensable for developmental and metabolic homeostasis, such as hyperactivation of pro-survival signaling axes, loss of suppressive regulations, and impaired functionalities of the immune system, have been extensively investigated aiming to understand the diversity of molecular mechanisms that underlie cancer development and progression. In this review, we intend to discuss the molecular mechanisms of how conventional physiological signal transduction confers to acquired drug resistance in cancer patients. We will particularly focus on protooncogenic receptor kinase inhibition-elicited tumor cell adaptation through two major core downstream signaling cascades, the PI3K/Akt and MAPK pathways. These pathways are crucial for cell growth and differentiation and are frequently hyperactivated during tumorigenesis. In addition, we also emphasize the emerging roles of the deregulated host immune system that may actively promote cancer progression and attenuate immunosurveillance in cancer therapies. Understanding these mechanisms may help to develop more effective therapeutic strategies that are able to keep the tumor in check and even possibly turn cancer into a chronic disease.
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Affiliation(s)
- Andreas Wicki
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Mario Mandalà
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Daniela Massi
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Daniela Taverna
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Huifang Tang
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Brian A. Hemmings
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
| | - Gongda Xue
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland; Department of Oncology and Hematology, Papa Giovanni XXIII Hospital, Bergamo, Italy; Department of Surgery and Translational Medicine, University of Florence, Florence, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy; Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, China; and Department of Mechanisms of Cancer, Friedrich Miescher Institute for
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114
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Prithviraj P, Anaka M, McKeown SJ, Permezel M, Walkiewicz M, Cebon J, Behren A, Jayachandran A. Pregnancy associated plasma protein-A links pregnancy and melanoma progression by promoting cellular migration and invasion. Oncotarget 2016; 6:15953-65. [PMID: 25940796 PMCID: PMC4599249 DOI: 10.18632/oncotarget.3643] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 03/23/2015] [Indexed: 11/25/2022] Open
Abstract
Melanoma is the most common cancer diagnosed in pregnant women and an aggressive course with poorer outcomes is commonly described during pregnancy or shortly after childbirth. The underlying mechanisms for this are not understood. Here, we report that melanoma migration, invasiveness and progression are promoted by pregnancy-associated plasma protein-A (PAPPA), a pregnancy-associated metalloproteinase produced by the placenta that increases the bioavailability of IGF1 by cleaving it from a circulating complex formed with IGFBP4. We show that PAPPA is widely expressed by metastatic melanoma tumors and is elevated in melanoma cells exhibiting mesenchymal, invasive and label-retaining phenotypes. Notably, inhibition of PAPPA significantly reduced invasion and migration of melanoma cells in vitro and in vivo within the embryonic chicken neural tube. PAPPA-enriched pregnancy serum treatment enhanced melanoma motility in vitro. Furthermore, we report that IGF1 can induce the phenotypic and functional effects of epithelial-to-mesenchymal transition (EMT) in melanoma cells. In this study, we establish a clear relationship between a pregnancy-associated protein PAPPA, melanoma and functional effects mediated through IGF1 that provides a plausible mechanism for accelerated melanoma progression during pregnancy. This opens the possibility of targeting the PAPPA/IGF1 axis therapeutically.
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Affiliation(s)
- Prashanth Prithviraj
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Cancer Immunobiology Laboratory, Heidelberg, VIC, Australia.,Olivia Newton-John Cancer Research Institute, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, VIC, Australia.,Department of Medicine, University of Melbourne, VIC, Australia
| | - Matthew Anaka
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Cancer Immunobiology Laboratory, Heidelberg, VIC, Australia
| | - Sonja J McKeown
- Department of Anatomy and Neuroscience, University of Melbourne, VIC, Australia
| | | | - Marzena Walkiewicz
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Cancer Immunobiology Laboratory, Heidelberg, VIC, Australia.,Olivia Newton-John Cancer Research Institute, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, VIC, Australia
| | - Jonathan Cebon
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Cancer Immunobiology Laboratory, Heidelberg, VIC, Australia.,Olivia Newton-John Cancer Research Institute, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, VIC, Australia.,Department of Medicine, University of Melbourne, VIC, Australia.,School of Cancer Medicine, La Trobe University, VIC, Australia
| | - Andreas Behren
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Cancer Immunobiology Laboratory, Heidelberg, VIC, Australia.,Olivia Newton-John Cancer Research Institute, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, VIC, Australia.,Department of Medicine, University of Melbourne, VIC, Australia.,School of Cancer Medicine, La Trobe University, VIC, Australia
| | - Aparna Jayachandran
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Cancer Immunobiology Laboratory, Heidelberg, VIC, Australia.,Olivia Newton-John Cancer Research Institute, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, VIC, Australia.,Department of Medicine, University of Melbourne, VIC, Australia.,School of Cancer Medicine, La Trobe University, VIC, Australia
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115
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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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116
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Dugo M, Nicolini G, Tragni G, Bersani I, Tomassetti A, Colonna V, Del Vecchio M, De Braud F, Canevari S, Anichini A, Sensi M. A melanoma subtype with intrinsic resistance to BRAF inhibition identified by receptor tyrosine kinases gene-driven classification. Oncotarget 2016; 6:5118-33. [PMID: 25742786 PMCID: PMC4467137 DOI: 10.18632/oncotarget.3007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/21/2014] [Indexed: 02/07/2023] Open
Abstract
Dysregulation of receptor tyrosine kinases (RTKs) contributes to several aspects of oncogenesis including drug resistance. In melanoma, distinct RTKs have been involved in BRAF inhibitors (BRAFi) resistance, yet the utility of RTKs expression pattern to identify intrinsically resistant tumors has not been assessed. Transcriptional profiling of RTKs and integration with a previous classification, reveals three robust subtypes in two independent datasets of melanoma cell lines and one cohort of melanoma samples. This classification was validated by Western blot in a panel of patient-derived melanoma cell lines. One of the subtypes identified here for the first time displayed the highest and lowest expression of EGFR and ERBB3, respectively, and included BRAF-mutant tumors all intrinsically resistant to BRAFi PLX4720, as assessed by analysis of the Cancer Cell Line Encyclopedia pharmacogenomic study and by in vitro growth inhibition assays. High levels of EGFR were detected, even before therapy, in tumor cells of one of three melanoma patients unresponsive to BRAFi. Use of different pharmacological inhibitors highlighted the relevance of PI3K/mTOR signaling for growth of this PLX4720-resistant subtype. Our results identify a specific molecular profile of melanomas intrinsically resistant to BRAFi and suggest the PI3K/mTOR pathway as a potential therapeutic target for these tumors.
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Affiliation(s)
- Matteo Dugo
- Functional Genomics and Bioinformatics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gabriella Nicolini
- Unit of Immunobiology of Human Tumors, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gabrina Tragni
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ilaria Bersani
- Unit of Immunobiology of Human Tumors, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Antonella Tomassetti
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Valentina Colonna
- Department of Clinical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Michele Del Vecchio
- Department of Clinical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Filippo De Braud
- Department of Clinical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvana Canevari
- Functional Genomics and Bioinformatics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Anichini
- Unit of Immunobiology of Human Tumors, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marialuisa Sensi
- Functional Genomics and Bioinformatics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Unit of Immunobiology of Human Tumors, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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117
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Jayachandran A, Lo PH, Chueh AC, Prithviraj P, Molania R, Davalos-Salas M, Anaka M, Walkiewicz M, Cebon J, Behren A. Transketolase-like 1 ectopic expression is associated with DNA hypomethylation and induces the Warburg effect in melanoma cells. BMC Cancer 2016; 16:134. [PMID: 26907172 PMCID: PMC4763451 DOI: 10.1186/s12885-016-2185-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 02/16/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND The metabolism of cancer cells is often reprogrammed by dysregulation of metabolic enzymes. Transketolase-like 1 (TKTL1) is a homodimeric transketolase linking the pentose-phosphate pathway with the glycolytic pathway. It is generally silenced at a transcriptional level in somatic tissues. However, in human cancers its expression is associated with the acquisition of a glycolytic phenotype (the Warburg effect) by cancer cells that contributes to the progression of malignant tumors. In melanoma, defective promoter methylation results in the expression of genes and their products that can affect the tumor cell's phenotype including the modification of immune and functional characteristics. The present study evaluates the role of TKTL1 as a mediator of disease progression in melanoma associated with a defective methylation phenotype. METHODS The expression of TKTL1 in metastatic melanoma tumors and cell lines was analysed by qRT-PCR and immunohistochemistry. The promoter methylation status of TKTL1 in melanoma cells was evaluated by quantitative methylation specific PCR. Using qRT-PCR, the effect of a DNA demethylating agent 5-aza-2'-deoxycytidine (5aza) on the expression of TKTL1 was examined. Biochemical and molecular analyses such as glucose consumption, lactate production, invasion, proliferation and cell cycle progression together with ectopic expression and siRNA mediated knockdown were used to investigate the role of TKTL1 in melanoma cells. RESULTS Expression of TKTL1 was highly restricted in normal adult tissues and was overexpressed in a subset of metastatic melanoma tumors and derived cell lines. The TKTL1 promoter was activated by hypomethylation and treatment with 5aza induced TKTL1 expression in melanoma cells. Augmented expression of TKTL1 in melanoma cells was associated with a glycolytic phenotype. Loss and gain of function studies revealed that TKTL1 contributed to enhanced invasion of melanoma cells. CONCLUSIONS Our data provide evidence for an important role of TKTL1 in aerobic glycolysis and tumor promotion in melanoma that may result from defective promoter methylation. This epigenetic change may enable the natural selection of tumor cells with a metabolic phenotype and thereby provide a potential therapeutic target for a subset of melanoma tumors with elevated TKTL1 expression.
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Affiliation(s)
- Aparna Jayachandran
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.,Department of Medicine, University of Melbourne, Melbourne, VIC, 3010, Australia.,School of Cancer Medicine, Latrobe University, Melbourne, VIC, 3086, Australia.,School of Medicine and the Gallipoli Medical Research Foundation, The University of Queensland, Brisbane, QLD 4120, Australia
| | - Pu-Han Lo
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia
| | - Anderly C Chueh
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia.,ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Melbourne, 3010, Australia
| | - Prashanth Prithviraj
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.,Department of Medicine, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Ramyar Molania
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
| | - Mercedes Davalos-Salas
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
| | - Matthew Anaka
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia.,Department of Medicine, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Marzena Walkiewicz
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
| | - Jonathan Cebon
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.,Department of Medicine, University of Melbourne, Melbourne, VIC, 3010, Australia.,School of Cancer Medicine, Latrobe University, Melbourne, VIC, 3086, Australia
| | - Andreas Behren
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Heidelberg, VIC, 3084, Australia. .,Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia. .,Department of Medicine, University of Melbourne, Melbourne, VIC, 3010, Australia. .,School of Cancer Medicine, Latrobe University, Melbourne, VIC, 3086, Australia. .,Cancer Immuno-biology Laboratory, Olivia Newton-John Cancer Research Institute, Level 5, Olivia Newton-John Cancer and Wellness Centre, 145 Studley Road, Heidelberg, VIC, 3084, Australia.
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118
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Castiglione R, Ihle MA, Heydt C, Schultheis AM, Merkelbach-Bruse S, Mauch C, Büttner R. The impact of sequencing on diagnosis and treatment of malignant melanoma. Expert Rev Mol Diagn 2016; 16:423-33. [PMID: 26822148 DOI: 10.1586/14737159.2016.1147958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Melanoma is one of the clinically most important cancer types considering its high mortality rate and that it is commonly diagnosed in relatively young people. With the advent of targeted therapies and, more recently, immune checkpoint inhibitors, more treatment options are available resulting in higher patient survival rates. However, the successful application of these targeted therapies critically depends on the reliable detection of molecular aberrations. Today, massively parallel sequencing techniques enable us to analyze large sets of genes in a relatively short time. It has allowed increased knowledge of acquired somatic mutations in melanoma and has helped to identify new targets for personalized therapy, and potentially may help to predict response to immune therapies. Described here are the development of sequencing techniques, how their improvement has changed diagnosis, prognosis and management of malignant melanoma and the future perspectives of melanoma diagnostics in the routine clinical setting.
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Affiliation(s)
| | - Michaela A Ihle
- a Institute of Pathology , University Hospital Cologne , Cologne , Germany
| | - Carina Heydt
- a Institute of Pathology , University Hospital Cologne , Cologne , Germany
| | - Anne M Schultheis
- a Institute of Pathology , University Hospital Cologne , Cologne , Germany
| | | | - Cornelia Mauch
- b Clinic for Dermatology , University Hospital Cologne , Cologne , Germany
| | - Reinhard Büttner
- a Institute of Pathology , University Hospital Cologne , Cologne , Germany
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119
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Zand B, Previs RA, Zacharias NM, Rupaimoole R, Mitamura T, Nagaraja AS, Guindani M, Dalton HJ, Yang L, Baddour J, Achreja A, Hu W, Pecot CV, Ivan C, Wu SY, McCullough CR, Gharpure KM, Shoshan E, Pradeep S, Mangala LS, Rodriguez-Aguayo C, Wang Y, Nick AM, Davies MA, Armaiz-Pena G, Liu J, Lutgendorf SK, Baggerly KA, Eli MB, Lopez-Berestein G, Nagrath D, Bhattacharya PK, Sood AK. Role of Increased n-acetylaspartate Levels in Cancer. J Natl Cancer Inst 2016; 108:djv426. [PMID: 26819345 DOI: 10.1093/jnci/djv426] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 12/16/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The clinical and biological effects of metabolic alterations in cancer are not fully understood. METHODS In high-grade serous ovarian cancer (HGSOC) samples (n = 101), over 170 metabolites were profiled and compared with normal ovarian tissues (n = 15). To determine NAT8L gene expression across different cancer types, we analyzed the RNA expression of cancer types using RNASeqV2 data available from the open access The Cancer Genome Atlas (TCGA) website (http://www.cbioportal.org/public-portal/). Using NAT8L siRNA, molecular techniques and histological analysis, we determined cancer cell viability, proliferation, apoptosis, and tumor growth in in vitro and in vivo (n = 6-10 mice/group) settings. Data were analyzed with the Student's t test and Kaplan-Meier analysis. Statistical tests were two-sided. RESULTS Patients with high levels of tumoral NAA and its biosynthetic enzyme, aspartate N-acetyltransferase (NAT8L), had worse overall survival than patients with low levels of NAA and NAT8L. The overall survival duration of patients with higher-than-median NAA levels (3.6 years) was lower than that of patients with lower-than-median NAA levels (5.1 years, P = .03). High NAT8L gene expression in other cancers (melanoma, renal cell, breast, colon, and uterine cancers) was associated with worse overall survival. NAT8L silencing reduced cancer cell viability (HEYA8: control siRNA 90.61% ± 2.53, NAT8L siRNA 39.43% ± 3.00, P < .001; A2780: control siRNA 90.59% ± 2.53, NAT8L siRNA 7.44% ± 1.71, P < .001) and proliferation (HEYA8: control siRNA 74.83% ± 0.92, NAT8L siRNA 55.70% ± 1.54, P < .001; A2780: control siRNA 50.17% ± 4.13, NAT8L siRNA 26.52% ± 3.70, P < .001), which was rescued by addition of NAA. In orthotopic mouse models (ovarian cancer and melanoma), NAT8L silencing reduced tumor growth statistically significantly (A2780: control siRNA 0.52 g ± 0.15, NAT8L siRNA 0.08 g ± 0.17, P < .001; HEYA8: control siRNA 0.79 g ± 0.42, NAT8L siRNA 0.24 g ± 0.18, P = .008, A375-SM: control siRNA 0.55 g ± 0.22, NAT8L siRNA 0.21 g ± 0.17 g, P = .001). NAT8L silencing downregulated the anti-apoptotic pathway, which was mediated through FOXM1. CONCLUSION These findings indicate that the NAA pathway has a prominent role in promoting tumor growth and represents a valuable target for anticancer therapy.Altered energy metabolism is a hallmark of cancer (1). Proliferating cancer cells have much greater metabolic requirements than nonproliferating differentiated cells (2,3). Moreover, altered cancer metabolism elevates unique metabolic intermediates, which can promote cancer survival and progression (4,5). Furthermore, emerging evidence suggests that proliferating cancer cells exploit alternative metabolic pathways to meet their high demand for energy and to accumulate biomass (6-8).
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Affiliation(s)
- Behrouz Zand
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Rebecca A Previs
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Niki M Zacharias
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Rajesha Rupaimoole
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Takashi Mitamura
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Archana Sidalaghatta Nagaraja
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Michele Guindani
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Heather J Dalton
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Lifeng Yang
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Joelle Baddour
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Abhinav Achreja
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Wei Hu
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Chad V Pecot
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Cristina Ivan
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Sherry Y Wu
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Christopher R McCullough
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Kshipra M Gharpure
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Einav Shoshan
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Sunila Pradeep
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Lingegowda S Mangala
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Cristian Rodriguez-Aguayo
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Ying Wang
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Alpa M Nick
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Michael A Davies
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Guillermo Armaiz-Pena
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Jinsong Liu
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Susan K Lutgendorf
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Keith A Baggerly
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Menashe Bar Eli
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Gabriel Lopez-Berestein
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Deepak Nagrath
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Pratip K Bhattacharya
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX
| | - Anil K Sood
- Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX.
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Molecular techniques for predicting behaviour in melanocytic neoplasms. Pathology 2016; 48:142-6. [PMID: 27020386 DOI: 10.1016/j.pathol.2015.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/11/2015] [Indexed: 11/24/2022]
Abstract
Molecular tools are rapidly emerging as novel tools for clinicians caring for cancer patients. Roles for these assays in melanocytic neoplasms include diagnosis for histologically ambiguous tumors, prognosis for conventional melanoma, and theragnosis for advanced disease. The introduction of these molecular strategies is timely, as different therapeutic options are rapidly developing to treat melanoma. With the development of new and effective therapeutic options, it is more critical than ever to improve the discrimination between patients with aggressive disease and those with more indolent tumours. In this review, we will evaluate the traditional staging of melanoma and what are the likely greatest opportunities for improvement with molecular strategies. We will explore a number of molecular assays that are now commercially available for the assessment of melanocytic neoplasms, which include techniques such as fluorescence in situ hybridisation, comparative genomic hybridisation, mRNA expression profiling and next generation sequencing, and discuss the optimal utilisation of each of these assays.
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121
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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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122
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Lauss M, Ringnér M, Karlsson A, Harbst K, Busch C, Geisler J, Lønning PE, Staaf J, Jönsson G. DNA methylation subgroups in melanoma are associated with proliferative and immunological processes. BMC Med Genomics 2015; 8:73. [PMID: 26545983 PMCID: PMC4636848 DOI: 10.1186/s12920-015-0147-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 10/28/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND DNA methylation at CpG dinucleotides is modified in tumorigenesis with potential impact on transcriptional activity. METHODS We used the Illumina 450 K platform to evaluate DNA methylation patterns of 50 metastatic melanoma tumors, with matched gene expression data. RESULTS We identified three different methylation groups and validated the groups in independent data from The Cancer Genome Atlas. One group displayed hypermethylation of a developmental promoter set, genome-wide demethylation, increased proliferation and activity of the SWI/SNF complex. A second group had a methylation pattern resembling stromal and leukocyte cells, over-expressed an immune signature and had improved survival rates in metastatic tumors (p < 0.05). A third group had intermediate methylation levels and expressed both proliferative and immune signatures. The methylation groups corresponded to some degree with previously identified gene expression phenotypes. CONCLUSIONS Melanoma consists of divergent methylation groups that are distinguished by promoter methylation, proliferation and content of immunological cells.
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Affiliation(s)
- Martin Lauss
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, 221 85, Sweden.
| | - Markus Ringnér
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, 221 85, Sweden.
| | - Anna Karlsson
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, 221 85, Sweden.
| | - Katja Harbst
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, 221 85, Sweden.
| | - Christian Busch
- Section of Oncology, Department of Clinical Science, University of Bergen, Bergen, Norway. .,Department of Clinical Oncology, Haukeland University Hospital, Bergen, Norway.
| | - Jürgen Geisler
- Section of Oncology, Department of Clinical Science, University of Bergen, Bergen, Norway. .,Department of Clinical Oncology, Haukeland University Hospital, Bergen, Norway. .,Present Address: Department of Clinical Molecular Biology and Laboratory Sciences, Akershus University Hospital, Lørenskog, Norway.
| | - Per Eystein Lønning
- Section of Oncology, Department of Clinical Science, University of Bergen, Bergen, Norway. .,Department of Clinical Oncology, Haukeland University Hospital, Bergen, Norway. .,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Johan Staaf
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, 221 85, Sweden.
| | - Göran Jönsson
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, 221 85, Sweden.
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123
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Rambow F, Job B, Petit V, Gesbert F, Delmas V, Seberg H, Meurice G, Van Otterloo E, Dessen P, Robert C, Gautheret D, Cornell RA, Sarasin A, Larue L. New Functional Signatures for Understanding Melanoma Biology from Tumor Cell Lineage-Specific Analysis. Cell Rep 2015; 13:840-853. [PMID: 26489459 PMCID: PMC5970542 DOI: 10.1016/j.celrep.2015.09.037] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 05/30/2015] [Accepted: 09/14/2015] [Indexed: 01/08/2023] Open
Abstract
Molecular signatures specific to particular tumor types are required to design treatments for resistant tumors. However, it remains unclear whether tumors and corresponding cell lines used for drug development share such signatures. We developed similarity core analysis (SCA), a universal and unsupervised computational framework for extracting core molecular features common to tumors and cell lines. We applied SCA to mRNA/miRNA expression data from various sources, comparing melanoma cell lines and metastases. The signature obtained was associated with phenotypic characteristics in vitro, and the core genes CAPN3 and TRIM63 were implicated in melanoma cell migration/invasion. About 90% of the melanoma signature genes belong to an intrinsic network of transcription factors governing neural development (TFAP2A, DLX2, ALX1, MITF, PAX3, SOX10, LEF1, and GAS7) and miRNAs (211-5p, 221-3p, and 10a-5p). The SCA signature effectively discriminated between two subpopulations of melanoma patients differing in overall survival, and classified MEKi/BRAFi-resistant and -sensitive melanoma cell lines.
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Affiliation(s)
- Florian Rambow
- Institut Curie, Normal and Pathological Development of Melanocytes, 91405 Orsay, France; Centre National de la Recherche Scientifique (CNRS) UMR3347, 91405 Orsay, France; INSERM U1021, 91405 Orsay, France; Equipe Labellisée - Ligue Nationale contre le Cancer, 91405 Orsay, France
| | - Bastien Job
- Plateforme de Bioinformatique, UMS AMMICA, Gustave-Roussy, 94805 Villejuif, France
| | - Valérie Petit
- Institut Curie, Normal and Pathological Development of Melanocytes, 91405 Orsay, France; Centre National de la Recherche Scientifique (CNRS) UMR3347, 91405 Orsay, France; INSERM U1021, 91405 Orsay, France; Equipe Labellisée - Ligue Nationale contre le Cancer, 91405 Orsay, France
| | - Franck Gesbert
- Institut Curie, Normal and Pathological Development of Melanocytes, 91405 Orsay, France; Centre National de la Recherche Scientifique (CNRS) UMR3347, 91405 Orsay, France; INSERM U1021, 91405 Orsay, France; Equipe Labellisée - Ligue Nationale contre le Cancer, 91405 Orsay, France
| | - Véronique Delmas
- Institut Curie, Normal and Pathological Development of Melanocytes, 91405 Orsay, France; Centre National de la Recherche Scientifique (CNRS) UMR3347, 91405 Orsay, France; INSERM U1021, 91405 Orsay, France; Equipe Labellisée - Ligue Nationale contre le Cancer, 91405 Orsay, France
| | - Hannah Seberg
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Guillaume Meurice
- Plateforme de Bioinformatique, UMS AMMICA, Gustave-Roussy, 94805 Villejuif, France
| | - Eric Van Otterloo
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Philippe Dessen
- Plateforme de Bioinformatique, UMS AMMICA, Gustave-Roussy, 94805 Villejuif, France
| | | | - Daniel Gautheret
- Plateforme de Bioinformatique, UMS AMMICA, Gustave-Roussy, 94805 Villejuif, France
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Alain Sarasin
- Centre National de la Recherche Scientifique (CNRS) UMR8200, Gustave-Roussy and University Paris-Sud, 94805 Villejuif, France
| | - Lionel Larue
- Institut Curie, Normal and Pathological Development of Melanocytes, 91405 Orsay, France; Centre National de la Recherche Scientifique (CNRS) UMR3347, 91405 Orsay, France; INSERM U1021, 91405 Orsay, France; Equipe Labellisée - Ligue Nationale contre le Cancer, 91405 Orsay, France.
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124
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Geserick P, Wang J, Schilling R, Horn S, Harris PA, Bertin J, Gough PJ, Feoktistova M, Leverkus M. Absence of RIPK3 predicts necroptosis resistance in malignant melanoma. Cell Death Dis 2015; 6:e1884. [PMID: 26355347 PMCID: PMC4650439 DOI: 10.1038/cddis.2015.240] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/07/2015] [Accepted: 07/13/2015] [Indexed: 12/14/2022]
Abstract
Acquired or intrinsic resistance to apoptotic and necroptotic stimuli is considered a major hindrance of therapeutic success in malignant melanoma. Inhibitor of apoptosis proteins (IAPs) are important regulators of apoptotic and necroptotic cell death mediated by numerous cell death signalling platforms. In this report we investigated the impact of IAPs for cell death regulation in malignant melanoma. Suppression of IAPs strongly sensitized a panel of melanoma cells to death ligand-induced cell death, which, surprisingly, was largely mediated by apoptosis, as it was completely rescued by addition of caspase inhibitors. Interestingly, the absence of necroptosis signalling correlated with a lack of receptor-interacting protein kinase-3 (RIPK3) mRNA and protein expression in all cell lines, whereas primary melanocytes and cultured nevus cells strongly expressed RIPK3. Reconstitution of RIPK3, but not a RIPK3-kinase dead mutant in a set of melanoma cell lines overcame CD95L/IAP antagonist-induced necroptosis resistance independent of autocrine tumour necrosis factor secretion. Using specific inhibitors, functional studies revealed that RIPK3-mediated mixed-lineage kinase domain-like protein (MLKL) phosphorylation and necroptosis induction critically required receptor-interacting protein kinase-1 signalling. Furthermore, the inhibitor of mutant BRAF Dabrafenib, but not Vemurafenib, inhibited necroptosis in melanoma cells whenever RIPK3 is present. Our data suggest that loss of RIPK3 in melanoma and selective inhibition of the RIPK3/MLKL axis by BRAF inhibitor Dabrafenib, but not Vemurafenib, is critical to protect from necroptosis. Strategies that allow RIPK3 expression may allow unmasking the necroptotic signalling machinery in melanoma and points to reactivation of this pathway as a treatment option for metastatic melanoma.
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Affiliation(s)
- P Geserick
- Section of Molecular Dermatology, Department of Dermatology, Venerology and Allergology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany
| | - J Wang
- Section of Molecular Dermatology, Department of Dermatology, Venerology and Allergology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany.,Department for Dermatology and Allergology, University Hospital Aachen, RWTH Aachen, Aachen, Germany
| | - R Schilling
- Section of Molecular Dermatology, Department of Dermatology, Venerology and Allergology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany
| | - S Horn
- Section of Molecular Dermatology, Department of Dermatology, Venerology and Allergology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany
| | - P A Harris
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapeutic Area, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - J Bertin
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapeutic Area, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - P J Gough
- Pattern Recognition Receptor Discovery Performance Unit, Immuno-Inflammation Therapeutic Area, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - M Feoktistova
- Section of Molecular Dermatology, Department of Dermatology, Venerology and Allergology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany.,Department for Dermatology and Allergology, University Hospital Aachen, RWTH Aachen, Aachen, Germany
| | - M Leverkus
- Section of Molecular Dermatology, Department of Dermatology, Venerology and Allergology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany.,Department for Dermatology and Allergology, University Hospital Aachen, RWTH Aachen, Aachen, Germany
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125
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Yakovleva ME, Welinder C, Sugihara Y, Pawłowski K, Rezeli M, Wieslander E, Malm J, Marko-Varga G. Workflow for large-scale analysis of melanoma tissue samples. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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126
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Ramsdale R, Jorissen RN, Li FZ, Al-Obaidi S, Ward T, Sheppard KE, Bukczynska PE, Young RJ, Boyle SE, Shackleton M, Bollag G, Long GV, Tulchinsky E, Rizos H, Pearson RB, McArthur GA, Dhillon AS, Ferrao PT. The transcription cofactor c-JUN mediates phenotype switching and BRAF inhibitor resistance in melanoma. Sci Signal 2015; 8:ra82. [PMID: 26286024 DOI: 10.1126/scisignal.aab1111] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Most patients with BRAF-mutant metastatic melanoma display remarkable but incomplete and short-lived responses to inhibitors of the BRAF kinase or the mitogen-activated protein kinase kinase (MEK), collectively BRAF/MEK inhibitors. We found that inherent resistance to these agents in BRAF(V600)-mutant melanoma cell lines was associated with high abundance of c-JUN and characteristics of a mesenchymal-like phenotype. Early drug adaptation in drug-sensitive cell lines grown in culture or as xenografts, and in patient samples during therapy, was consistently characterized by down-regulation of SPROUTY4 (a negative feedback regulator of receptor tyrosine kinases and the BRAF-MEK signaling pathway), increased expression of JUN and reduced expression of LEF1. This coincided with a switch in phenotype that resembled an epithelial-mesenchymal transition (EMT). In cultured cells, these BRAF inhibitor-induced changes were reversed upon removal of the drug. Knockdown of SPROUTY4 was sufficient to increase the abundance of c-JUN in the absence of drug treatment. Overexpressing c-JUN in drug-naïve melanoma cells induced similar EMT-like phenotypic changes to BRAF inhibitor treatment, whereas knocking down JUN abrogated the BRAF inhibitor-induced early adaptive changes associated with resistance and enhanced cell death. Combining the BRAF inhibitor with an inhibitor of c-JUN amino-terminal kinase (JNK) reduced c-JUN phosphorylation, decreased cell migration, and increased cell death in melanoma cells. Gene expression data from a panel of melanoma cell lines and a patient cohort showed that JUN expression correlated with a mesenchymal gene signature, implicating c-JUN as a key mediator of the mesenchymal-like phenotype associated with drug resistance.
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Affiliation(s)
- Rachel Ramsdale
- Molecular Oncology Laboratory, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, Victoria 3002, Australia. Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Robert N Jorissen
- Systems Biology and Personalised Medicine Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, Victoria 3052, Australia. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia
| | - Frederic Z Li
- Molecular Oncology Laboratory, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, Victoria 3002, Australia. Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia
| | - Sheren Al-Obaidi
- Molecular Oncology Laboratory, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, Victoria 3002, Australia. Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Teresa Ward
- Molecular Oncology Laboratory, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, Victoria 3002, Australia. Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Karen E Sheppard
- Molecular Oncology Laboratory, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, Victoria 3002, Australia. Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia
| | - Patricia E Bukczynska
- Molecular Therapeutics and Biomarkers Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Richard J Young
- Molecular Therapeutics and Biomarkers Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Samantha E Boyle
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Cancer Development and Treatment Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia
| | - Mark Shackleton
- Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia. Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Cancer Development and Treatment Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia
| | - Gideon Bollag
- Plexxikon Inc., 91 Bolivar Drive, Berkeley, CA 94710, USA
| | - Georgina V Long
- Melanoma Institute Australia, Sydney, New South Wales 2060, Australia. University of Sydney, Sydney, New South Wales 2006, Australia
| | - Eugene Tulchinsky
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester LE2 7LX, UK
| | - Helen Rizos
- Melanoma Institute Australia, Sydney, New South Wales 2060, Australia. Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Richard B Pearson
- Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia. Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia. Cancer Signalling Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Grant A McArthur
- Molecular Oncology Laboratory, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, Victoria 3002, Australia. Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia. Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
| | - Amardeep S Dhillon
- Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia. Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia
| | - Petranel T Ferrao
- Molecular Oncology Laboratory, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, Victoria 3002, Australia. Oncogenic Signalling and Growth Control Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia. Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia. Department of Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Victoria 3010, Australia.
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Yélamos O, Gerami P. Predicting the outcome of melanoma: can we tell the future of a patient's melanoma? Melanoma Manag 2015; 2:217-224. [PMID: 30190851 PMCID: PMC6094684 DOI: 10.2217/mmt.15.15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cutaneous melanoma is responsible for the greatest number of skin cancer related deaths. For many years there were few therapeutic options. However, in the last years a number of new therapeutic options have emerged showing improved survival rates for advanced melanoma patients. A significant question based on these findings is whether identification and treatment of patients with biologically aggressive melanomas at an earlier clinical stage offer an opportunity for even greater improvement in overall survival. In this review, we will discuss the recent advancements in molecular strategies beyond traditional staging to identify biologically aggressive melanomas, and which are their implications in terms of predicting the prognosis of patients with melanoma.
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Affiliation(s)
- Oriol Yélamos
- Department of Dermatology, Feinberg School of Medicine, The Robert H Lurie Cancer Center, Northwestern University, 676 N. St Clair Street, Suite 1765, Chicago, IL 60611, USA
| | - Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, The Robert H Lurie Cancer Center, Northwestern University, 676 N. St Clair Street, Suite 1765, Chicago, IL 60611, USA
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128
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Stewart EL, Mascaux C, Pham NA, Sakashita S, Sykes J, Kim L, Yanagawa N, Allo G, Ishizawa K, Wang D, Zhu CQ, Li M, Ng C, Liu N, Pintilie M, Martin P, John T, Jurisica I, Leighl NB, Neel BG, Waddell TK, Shepherd FA, Liu G, Tsao MS. Clinical Utility of Patient-Derived Xenografts to Determine Biomarkers of Prognosis and Map Resistance Pathways in EGFR-Mutant Lung Adenocarcinoma. J Clin Oncol 2015; 33:2472-80. [PMID: 26124487 DOI: 10.1200/jco.2014.60.1492] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Although epidermal growth factor receptor (EGFR) -mutated adenocarcinomas initially have high response rates to EGFR tyrosine kinase inhibitors (TKIs), most patients eventually develop resistance. Patient-derived xenografts (PDXs) are considered preferred preclinical models to study the biology of patient tumors. EGFR-mutant PDX models may be valuable tools to study the biology of these tumors and to elucidate mechanisms of resistance to EGFR-targeted therapies. METHODS Surgically resected early-stage non-small-cell lung carcinoma (NSCLC) tumors were implanted into nonobese diabetic severe combined immune deficient (NOD-SCID) mice. EGFR TKI treatment was initiated at tumor volumes of 150 μL. Gene expression analysis was performed using a microarray platform. RESULTS Of 33 lung adenocarcinomas with EGFR activating mutations, only 6 (18%) engrafted and could be propagated beyond passage one. Engraftment was associated with upregulation of genes involved in mitotic checkpoint and cell proliferation. A differentially expressed gene set between engrafting and nonengrafting patients could identify patients harboring EGFR-mutant tumor with significantly different prognoses in The Cancer Genome Atlas Lung Adenocarcinoma datasets. The PDXs included models with variable sensitivity to first- and second-generation EGFR TKIs and the monoclonal antibody cetuximab. All EGFR-mutant NSCLC PDXs studied closely recapitulated their corresponding patient tumor phenotype and clinical course, including response pattern to EGFR TKIs. CONCLUSION PDX models closely recapitulate primary tumor biology and clinical outcome. They may serve as important laboratory models to investigate mechanisms of resistance to targeted therapies, and for preclinical testing of novel treatment strategies.
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Affiliation(s)
- Erin L Stewart
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Celine Mascaux
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Nhu-An Pham
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Shingo Sakashita
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Jenna Sykes
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Lucia Kim
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Naoki Yanagawa
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Ghassan Allo
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Kota Ishizawa
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Dennis Wang
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Chang-Qi Zhu
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Ming Li
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Christine Ng
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Ni Liu
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Melania Pintilie
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Petra Martin
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Tom John
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Igor Jurisica
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Natasha B Leighl
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Benjamin G Neel
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Thomas K Waddell
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Frances A Shepherd
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Geoffrey Liu
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia
| | - Ming-Sound Tsao
- Erin L. Stewart, Celine Mascaux, Nhu-An Pham, Shingo Sakashita, Jenna Sykes, Lucia Kim, Naoki Yanagawa, Ghassan Allo, Kota Ishizawa, Dennis Wang, Chang-Qi Zhu, Ming Li, Christine Ng, Ni Liu, Melania Pintilie, Petra Martin, Tom John, Igor Jurisica, Natasha B. Leighl, Benjamin G. Neel, Thomas K. Waddell, Frances A. Shepherd, Geoffrey Liu, Ming-Sound Tsao, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada; Lucia Kim, Inha University College of Medicine, Incheon, South Korea; and Tom John, Austin Hospital, Heidelberg, Australia.
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129
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Nsengimana J, Laye J, Filia A, Walker C, Jewell R, Van den Oord JJ, Wolter P, Patel P, Sucker A, Schadendorf D, Jönsson GB, Bishop DT, Newton-Bishop J. Independent replication of a melanoma subtype gene signature and evaluation of its prognostic value and biological correlates in a population cohort. Oncotarget 2015; 6:11683-93. [PMID: 25871393 PMCID: PMC4484486 DOI: 10.18632/oncotarget.3549] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/10/2015] [Indexed: 12/05/2022] Open
Abstract
Development and validation of robust molecular biomarkers has so far been limited in melanoma research. In this paper we used a large population-based cohort to replicate two published gene signatures for melanoma classification. We assessed the signatures prognostic value and explored their biological significance by correlating them with factors known to be associated with survival (vitamin D) or etiological routes (nevi, sun sensitivity and telomere length). Genomewide microarray gene expressions were profiled in 300 archived tumors (224 primaries, 76 secondaries). The two gene signatures classified up to 96% of our samples and showed strong correlation with melanoma specific survival (P=3 x 10(-4)), Breslow thickness (P=5 x 10(-10)), ulceration (P=9.x10-8) and mitotic rate (P=3 x 10(-7)), adding prognostic value over AJCC stage (adjusted hazard ratio 1.79, 95%CI 1.13-2.83), as previously reported. Furthermore, molecular subtypes were associated with season-adjusted serum vitamin D at diagnosis (P=0.04) and genetically predicted telomere length (P=0.03). Specifically, molecular high-grade tumors were more frequent in patients with lower vitamin D levels whereas high immune tumors came from patients with predicted shorter telomeres. Our data confirm the utility of molecular biomarkers in melanoma prognostic estimation using tiny archived specimens and shed light on biological mechanisms likely to impact on cancer initiation and progression.
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Affiliation(s)
- Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Jon Laye
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Anastasia Filia
- National Heart and Lung Institute, Imperial College, London, UK
| | - Christy Walker
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Rosalyn Jewell
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Joost J Van den Oord
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
- European Organisation for Research and Treatment of Cancer (EORTC) Melanoma Group, Brussels, Belgium
| | - Pascal Wolter
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Poulam Patel
- School of Medicine, University of Nottingham, Nottingham, UK
- European Organisation for Research and Treatment of Cancer (EORTC) Melanoma Group, Brussels, Belgium
| | - Antje Sucker
- Department of Dermatology, Essen University Hospital, Essen, and German Consortium of Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, Essen University Hospital, Essen, and German Consortium of Translational Cancer Research (DKTK), Heidelberg, Germany
- European Organisation for Research and Treatment of Cancer (EORTC) Melanoma Group, Brussels, Belgium
| | - Göran B Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
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130
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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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Twyman-Saint Victor C, Rech AJ, Maity A, Rengan R, Pauken KE, Stelekati E, Benci JL, Xu B, Dada H, Odorizzi PM, Herati RS, Mansfield KD, Patsch D, Amaravadi RK, Schuchter LM, Ishwaran H, Mick R, Pryma DA, Xu X, Feldman MD, Gangadhar TC, Hahn SM, Wherry EJ, Vonderheide RH, Minn AJ. Radiation and dual checkpoint blockade activate non-redundant immune mechanisms in cancer. Nature 2015; 520:373-7. [PMID: 25754329 PMCID: PMC4401634 DOI: 10.1038/nature14292] [Citation(s) in RCA: 1751] [Impact Index Per Article: 194.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 02/09/2015] [Indexed: 02/07/2023]
Abstract
Immune checkpoint inhibitors1 result in impressive clinical responses2–5 but optimal results will require combination with each other6 and other therapies. This raises fundamental questions about mechanisms of non-redundancy and resistance. Here, we report major tumor regressions in a subset of patients with metastatic melanoma treated with an anti-CTLA4 antibody (anti-CTLA4) and radiation (RT) and reproduced this effect in mouse models. Although combined treatment improved responses in irradiated and unirradiated tumors, resistance was common. Unbiased analyses of mice revealed that resistance was due to upregulation of PD-L1 on melanoma cells and associated with T cell exhaustion. Accordingly, optimal response in melanoma and other cancer types requires RT, anti-CTLA4, and anti-PD-L1/PD-1. Anti-CTLA4 predominantly inhibits T regulatory cells (Tregs) to increase the CD8 T cell to Treg (CD8/Treg) ratio. RT enhances the diversity of the T cell receptor (TCR) repertoire of intratumoral T cells. Together, anti-CTLA4 promotes expansion of T cells, while RT shapes the TCR repertoire of the expanded peripheral clones. Addition of PD-L1 blockade reverses T cell exhaustion to mitigate depression in the CD8/Treg ratio and further encourages oligo-clonal T cell expansion. Similar to results from mice, patients on our clinical trial with melanoma showing high PD-L1 did not respond to RT + anti-CTLA4, demonstrated persistent T cell exhaustion, and rapidly progressed. Thus, PD-L1 on melanoma cells allows tumors to escape anti-CTLA4-based therapy, and the combination of RT, anti-CTLA4, and anti-PD-L1 promotes response and immunity through distinct mechanisms.
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Affiliation(s)
- Christina Twyman-Saint Victor
- 1] Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew J Rech
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Amit Maity
- 1] Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ramesh Rengan
- 1] Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen E Pauken
- 1] Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Erietta Stelekati
- 1] Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joseph L Benci
- 1] Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Bihui Xu
- 1] Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hannah Dada
- 1] Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Pamela M Odorizzi
- 1] Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ramin S Herati
- 1] Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kathleen D Mansfield
- 1] Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dana Patsch
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ravi K Amaravadi
- 1] Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lynn M Schuchter
- 1] Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Hemant Ishwaran
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miami, Florida 33136, USA
| | - Rosemarie Mick
- 1] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Daniel A Pryma
- 1] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xiaowei Xu
- 1] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael D Feldman
- 1] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Tara C Gangadhar
- 1] Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Stephen M Hahn
- 1] Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - E John Wherry
- 1] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [3] Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Robert H Vonderheide
- 1] Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [3] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [4] Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andy J Minn
- 1] Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [3] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [4] Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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132
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Howlin J, Cirenajwis H, Lettiero B, Staaf J, Lauss M, Saal L, Borg Å, Gruvberger-Saal S, Jönsson G. Loss of CITED1, an MITF regulator, drives a phenotype switch in vitro and can predict clinical outcome in primary melanoma tumours. PeerJ 2015; 3:e788. [PMID: 25755924 PMCID: PMC4349148 DOI: 10.7717/peerj.788] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/04/2015] [Indexed: 12/15/2022] Open
Abstract
CITED1 is a non-DNA binding transcriptional co-regulator whose expression can distinguish the ‘proliferative’ from ‘invasive’ signature in the phenotype-switching model of melanoma. We have found that, in addition to other ‘proliferative’ signature genes, CITED1 expression is repressed by TGFβ while the ‘invasive’ signature genes are upregulated. In agreement, CITED1 positively correlates with MITF expression and can discriminate the MITF-high/pigmentation tumour molecular subtype in a large cohort (120) of melanoma cell lines. Interestingly, CITED1 overexpression significantly suppressed MITF promoter activation, mRNA and protein expression levels while MITF was transiently upregulated following siRNA mediated CITED1 silencing. Conversely, MITF siRNA silencing resulted in CITED1 downregulation indicating a reciprocal relationship. Whole genome expression analysis identified a phenotype shift induced by CITED1 silencing and driven mainly by expression of MITF and a cohort of MITF target genes that were significantly altered. Concomitantly, we found changes in the cell-cycle profile that manifest as transient G1 accumulation, increased expression of CDKN1A and a reduction in cell viability. Additionally, we could predict survival outcome by classifying primary melanoma tumours using our in vitro derived ‘CITED1-silenced’ gene expression signature. We hypothesize that CITED1 acts a regulator of MITF, functioning to maintain MITF levels in a range compatible with tumourigenesis.
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Affiliation(s)
- Jillian Howlin
- Division of Oncology-Pathology, Lund University Cancer Center/Medicon Village, Scheelevägen, Lund, Sweden.,Cell and Experimental Pathology, Department of Laboratory Medicine Malmö, Lund University, Sweden
| | - Helena Cirenajwis
- Division of Oncology-Pathology, Lund University Cancer Center/Medicon Village, Scheelevägen, Lund, Sweden
| | - Barbara Lettiero
- Division of Oncology-Pathology, Lund University Cancer Center/Medicon Village, Scheelevägen, Lund, Sweden
| | - Johan Staaf
- Division of Oncology-Pathology, Lund University Cancer Center/Medicon Village, Scheelevägen, Lund, Sweden
| | - Martin Lauss
- Division of Oncology-Pathology, Lund University Cancer Center/Medicon Village, Scheelevägen, Lund, Sweden
| | - Lao Saal
- Division of Oncology-Pathology, Lund University Cancer Center/Medicon Village, Scheelevägen, Lund, Sweden
| | - Åke Borg
- Division of Oncology-Pathology, Lund University Cancer Center/Medicon Village, Scheelevägen, Lund, Sweden
| | - Sofia Gruvberger-Saal
- Division of Oncology-Pathology, Lund University Cancer Center/Medicon Village, Scheelevägen, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology-Pathology, Lund University Cancer Center/Medicon Village, Scheelevägen, Lund, Sweden
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133
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Genome-Wide DNA Methylation Analysis in Melanoma Reveals the Importance of CpG Methylation in MITF Regulation. J Invest Dermatol 2015; 135:1820-1828. [PMID: 25705847 DOI: 10.1038/jid.2015.61] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 12/15/2022]
Abstract
The microphthalmia-associated transcription factor (MITF) is a key regulator of melanocyte development and a lineage-specific oncogene in melanoma; a highly lethal cancer known for its unpredictable clinical course. MITF is regulated by multiple intracellular signaling pathways, although the exact mechanisms that determine MITF expression and activity remain incompletely understood. In this study, we obtained genome-wide DNA methylation profiles from 50 stage IV melanomas, normal melanocytes, keratinocytes, and dermal fibroblasts and utilized The Cancer Genome Atlas data for experimental validation. By integrating DNA methylation and gene expression data, we found that hypermethylation of MITF and its co-regulated differentiation pathway genes corresponded to decreased gene expression levels. In cell lines with a hypermethylated MITF-pathway, overexpression of MITF did not alter the expression level or methylation status of the MITF pathway genes. In contrast, however, demethylation treatment of these cell lines induced MITF-pathway activity, confirming that gene regulation was controlled via methylation. The discovery that the activity of the master regulator of pigmentation, MITF, and its downstream targets may be regulated by hypermethylation has significant implications for understanding the development and evolvement of melanoma.
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134
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USP11-dependent selective cIAP2 deubiquitylation and stabilization determine sensitivity to Smac mimetics. Cell Death Differ 2015; 22:1463-76. [PMID: 25613375 DOI: 10.1038/cdd.2014.234] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 12/22/2022] Open
Abstract
Given their crucial role in apoptosis suppression, inhibitor of apoptosis proteins (IAPs) have recently become attractive targets for cancer therapy. Here, we report that cellular IAP2 (cIAP2) is specifically stabilized in several cancer cell lines, leading to resistance to Smac mimetics, such as BV6 and birinapant. In particular, our results showed that cIAP2 depletion, but not cIAP1 depletion, sensitized cancer cells to Smac mimetic-induced apoptosis. Ubiquitin-specific protease 11 (USP11) is a deubiquitylase that directly stabilizes cIAP2. USP11 overexpression is frequently found in colorectal cancer and melanoma and is correlated with poor survival. In our study, cancer cell lines expressing high levels of USP11 exhibited strong resistance to Smac mimetic-induced cIAP2 degradation. Furthermore, USP11 downregulation sensitized these cells to apoptosis induced by TRAIL and BV6 and suppressed tumor growth in a xenograft model. Finally, the TNFα/JNK pathway induced USP11 expression and maintained cIAP2 stability, suggesting an alternative TNFα-dependent cell survival pathway. Collectively, our data suggest that USP11-stabilized cIAP2 may serve as a barrier against IAP-targeted clinical approaches.
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135
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Abstract
The last few years have witnessed the dawn of the molecular era in melanoma treatment. With the advent of successful therapy targeting mutant BRAF, melanoma is leading the field of cancer research in the molecular approach to therapy of advanced disease. Attempting to keep pace with advances in therapy are advances in the molecular assessment of melanoma progression, facilitated by the availability of genome-wide approaches to interrogate the malignant phenotype. At the DNA level, this has included approaches such as comparative genomic hybridization. At the RNA level, this has consisted of gene expression profiling using various assay methodologies. In certain instances, markers identified using these platforms have been further examined and developed using fluorescence in situ hybridization and immunohistochemical analysis. In this article, we will review recent progress in the development of novel molecular markers for melanoma that are nearing clinical application. We will review developments in the molecular classification of melanoma, in the molecular diagnosis of melanoma, and in the molecular assessment of melanoma prognosis.
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Affiliation(s)
- M Kashani-Sabet
- Center for Melanoma Research and Treatment, California Pacific Medical Center Research Institute, 475 Brannan St., Suite 220, San Francisco, CA, 94107, U.S.A
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136
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Ilieva KM, Correa I, Josephs DH, Karagiannis P, Egbuniwe IU, Cafferkey MJ, Spicer JF, Harries M, Nestle FO, Lacy KE, Karagiannis SN. Effects of BRAF mutations and BRAF inhibition on immune responses to melanoma. Mol Cancer Ther 2014; 13:2769-83. [PMID: 25385327 DOI: 10.1158/1535-7163.mct-14-0290] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Malignant melanoma is associated with poor clinical prognosis; however, novel molecular and immune therapies are now improving patient outcomes. Almost 50% of melanomas harbor targetable activating mutations of BRAF that promote RAS-RAF-MEK-ERK pathway activation and melanoma proliferation. Recent evidence also indicates that melanomas bearing mutant BRAF may also have altered immune responses, suggesting additional avenues for treatment of this patient group. The small molecule inhibitors selective for mutant BRAF induce significant but short-lived clinical responses in a proportion of patients, but also lead to immune stimulatory bystander events, which then subside with the emergence of resistance to inhibition. Simultaneous BRAF and MEK inhibition, and especially combination of BRAF inhibitors with new immunotherapies such as checkpoint blockade antibodies, may further enhance immune activation, or counteract immunosuppressive signals. Preclinical evaluation and ongoing clinical trials should provide novel insights into the role of immunity in the therapy of BRAF-mutant melanoma.
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Affiliation(s)
- Kristina M Ilieva
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine and NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London, United Kingdom
| | - Isabel Correa
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine and NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London, United Kingdom
| | - Debra H Josephs
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine and NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London, United Kingdom. Department of Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, London, United Kingdom
| | - Panagiotis Karagiannis
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine and NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London, United Kingdom
| | - Isioma U Egbuniwe
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine and NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London, United Kingdom
| | - Michiala J Cafferkey
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine and NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London, United Kingdom
| | - James F Spicer
- Department of Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, London, United Kingdom
| | - Mark Harries
- Clinical Oncology, Guy's and St. Thomas's NHS Foundation Trust, Guy's Hospital, London, United Kingdom
| | - Frank O Nestle
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine and NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London, United Kingdom
| | - Katie E Lacy
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine and NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London, United Kingdom
| | - Sophia N Karagiannis
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine and NIHR Biomedical Research Centre at Guy's and St. Thomas's Hospitals and King's College London, London, United Kingdom.
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137
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Performance comparison of three BRAF V600E detection methods in malignant melanoma and colorectal cancer specimens. Tumour Biol 2014; 36:1003-13. [PMID: 25318602 PMCID: PMC4342512 DOI: 10.1007/s13277-014-2711-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/05/2014] [Indexed: 02/02/2023] Open
Abstract
Personalized cancer care requires reliable biomarkers. While the BRAF V600E mutation is implemented in the clinic, no method for its detection has so far been established as reference. We aimed to perform a comprehensive comparison of three methods currently being used for V600E detection in clinical samples. We analysed genomic DNA from 127 malignant melanomas (77 patients) and 389 tumours from 141 colorectal cancer patients (383 liver metastases and 6 primary tumours) by Sanger sequencing and a single probe-based high-resolution melting assay (LightMix). Formalin-fixed paraffin-embedded (FFPE) tissue from a subset of these lesions (n = 77 and 304, respectively) was analysed by immunohistochemistry (IHC) using the V600E-specific antibody VE1. In a dilution series of V600E-mutated DNA in wild-type DNA, the detection limit for the LightMix assay was 1:1000 mutated alleles while it was 1:10 for Sanger sequencing. In line with this, we detected 15 additional mutated melanoma samples and two additional mutated metastatic colorectal cancer samples by the LightMix assay compared to Sanger sequencing. For the melanoma samples, we observed high concordance between DNA-based methods and analysis by IHC. However, in colorectal samples, IHC performed poorly with 12 samples being scored as V600E positive exclusively by IHC and nine samples being scored as V600E negative exclusively by IHC. In conclusion, the VE1 antibody is not recommendable for clinical tests of colorectal cancer samples. For melanoma samples, IHC may be useful as a screening tool guiding further analytical approaches.
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138
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Linsley PS, Speake C, Whalen E, Chaussabel D. Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis. PLoS One 2014; 9:e109760. [PMID: 25314013 PMCID: PMC4196925 DOI: 10.1371/journal.pone.0109760] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/03/2014] [Indexed: 12/27/2022] Open
Abstract
While immunotherapies are rapidly becoming mainstays of cancer treatment, significant gaps remain in our understanding of how to optimally target them, alone or in combination. Here we describe a novel method to monitor levels of immune cells and pathways in expression data from solid tumors using pre-defined groups or modules of co-regulated immune genes. We show that expression of an interconnected sub-network of type I interferon-stimulated genes (ISGs) in melanomas at the time of diagnosis significantly predicted patient survival, as did, to a lesser extent, sub-networks of T helper/T regulatory and NK/T Cytotoxic cell genes. As a group, poor prognosis tumors with reduced ISG and immune gene levels exhibited significant copy number loss of the interferon gene cluster located at chromosome 9p21.3. Our studies demonstrate a link between type I interferon action and immune cell levels in melanomas, and suggest that therapeutic approaches augmenting both activities may be most beneficial.
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Affiliation(s)
- Peter S. Linsley
- Department of Systems Immunology, Benaroya Research Institute, Seattle, WA, United States of America
- * E-mail:
| | - Cate Speake
- Department of Systems Immunology, Benaroya Research Institute, Seattle, WA, United States of America
| | - Elizabeth Whalen
- Department of Systems Immunology, Benaroya Research Institute, Seattle, WA, United States of America
| | - Damien Chaussabel
- Department of Systems Immunology, Benaroya Research Institute, Seattle, WA, United States of America
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139
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Karlsson A, Jönsson M, Lauss M, Brunnström H, Jönsson P, Borg Å, Jönsson G, Ringnér M, Planck M, Staaf J. Genome-wide DNA methylation analysis of lung carcinoma reveals one neuroendocrine and four adenocarcinoma epitypes associated with patient outcome. Clin Cancer Res 2014; 20:6127-40. [PMID: 25278450 DOI: 10.1158/1078-0432.ccr-14-1087] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Lung cancer is the worldwide leading cause of death from cancer. DNA methylation in gene promoter regions is a major mechanism of gene expression regulation that may promote tumorigenesis. However, whether clinically relevant subgroups based on DNA methylation patterns exist in lung cancer remains unclear. EXPERIMENTAL DESIGN Whole-genome DNA methylation analysis using 450K Illumina BeadArrays was performed on 12 normal lung tissues and 124 tumors, including 83 adenocarcinomas, 23 squamous cell carcinomas (SqCC), 1 adenosquamous cancer, 5 large cell carcinomas, 9 large cell neuroendocrine carcinomas (LCNEC), and 3 small-cell carcinomas (SCLC). Unsupervised bootstrap clustering was performed to identify DNA methylation subgroups, which were validated in 695 adenocarcinomas and 122 SqCCs. Subgroups were characterized by clinicopathologic factors, whole-exome sequencing data, and gene expression profiles. RESULTS Unsupervised analysis identified five DNA methylation subgroups (epitypes). One epitype was distinctly associated with neuroendocrine tumors (LCNEC and SCLC). For adenocarcinoma, remaining four epitypes were associated with unsupervised and supervised gene expression phenotypes, and differences in molecular features, including global hypomethylation, promoter hypermethylation, genomic instability, expression of proliferation-associated genes, and mutations in KRAS, TP53, KEAP1, SMARCA4, and STK11. Furthermore, these epitypes were associated with clinicopathologic features such as smoking history and patient outcome. CONCLUSIONS Our findings highlight one neuroendocrine and four adenocarcinoma epitypes associated with molecular and clinicopathologic characteristics, including patient outcome. This study demonstrates the possibility to further subgroup lung cancer, and more specifically adenocarcinomas, based on epigenetic/molecular classification that could lead to more accurate tumor classification, prognostication, and tailored patient therapy.
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Affiliation(s)
- Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Martin Lauss
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Hans Brunnström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Per Jönsson
- Department of Thoracic Surgery, Lund University and Skåne University Hospital, Lund, Sweden
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden.
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140
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Dai M, Yip YY, Hellstrom I, Hellstrom KE. Curing mice with large tumors by locally delivering combinations of immunomodulatory antibodies. Clin Cancer Res 2014; 21:1127-38. [PMID: 25142145 DOI: 10.1158/1078-0432.ccr-14-1339] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
PURPOSE Immunomodulatory mAbs can treat cancer, but cures are rare except for small tumors. Our objective was to explore whether the therapeutic window increases by combining mAbs with different modes of action and injecting them into tumors. EXPERIMENTAL DESIGN Combinations of mAbs to CD137/PD-1/CTLA-4 or CD137/PD-1/CTLA-4/CD19 were administrated intratumorally to mice with syngeneic tumors (B16 and SW1 melanoma, TC1 lung carcinoma), including tumors with a mean surface of approximately 80 mm(2). Survival and tumor growth were assessed. Immunologic responses were evaluated using flow cytometry and qRT-PCR. RESULTS More than 50% of tumor-bearing mice had complete regression and long-term survival after tumor injection with mAbs recognizing CD137/PD-1/CTLA-4/CD19 with similar responses in three models. Intratumoral injection was more efficacious than intraperitoneal injection in causing rejection also of untreated tumors in the same mice. The three-mAb combination could also induce regression, but was less efficacious. There were few side effects, and therapy-resistant tumors were not observed. Transplanted tumor cells rapidly caused a Th2 response with increased CD19 cells. Successful therapy shifted this response to the Th1 phenotype with decreased CD19 cells and increased numbers of long-term memory CD8 effector cells and T cells making IFNγ and TNFα. CONCLUSIONS Intratumoral injection of mAbs recognizing CD137/PD-1/CTLA-4/CD19 can eradicate established tumors and reverse a Th2 response with tumor-associated CD19 cells to Th1 immunity, whereas a combination lacking anti-CD19 is less effective. There are several human cancers for which a similar approach may provide clinical benefit.
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Affiliation(s)
- Min Dai
- University of Washington Harborview Medical Center, Department of Pathology, Seattle, Washington
| | - Yuen Yee Yip
- University of Washington Harborview Medical Center, Department of Pathology, Seattle, Washington
| | - Ingegerd Hellstrom
- University of Washington Harborview Medical Center, Department of Pathology, Seattle, Washington
| | - Karl Erik Hellstrom
- University of Washington Harborview Medical Center, Department of Pathology, Seattle, Washington.
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141
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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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142
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Tomei S, Bedognetti D, De Giorgi V, Sommariva M, Civini S, Reinboth J, Al Hashmi M, Ascierto ML, Liu Q, Ayotte BD, Worschech A, Uccellini L, Ascierto PA, Stroncek D, Palmieri G, Chouchane L, Wang E, Marincola FM. The immune-related role of BRAF in melanoma. Mol Oncol 2014; 9:93-104. [PMID: 25174651 PMCID: PMC4500792 DOI: 10.1016/j.molonc.2014.07.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 07/08/2014] [Accepted: 07/17/2014] [Indexed: 11/17/2022] Open
Abstract
Background The existence of a dichotomy between immunologically active and quiescent tumor phenotypes has been recently recognized in several types of cancer. The activation of a Th1 type of immune signature has been shown to confer better prognosis and likelihood to respond to immunotherapy. However, whether such dichotomy depends on the genetic make‐up of individual cancers is not known yet. BRAF and NRAS mutations are commonly acquired during melanoma progression. Here we explored the role of BRAF and NRAS mutations in influencing the immune phenotype based on a classification previously identified by our group. Methods One‐hundred‐thirteen melanoma metastases underwent microarray analysis and BRAF and NRAS genotyping. Allele‐specific PCR was also performed in order to exclude low‐frequency mutations. Results Comparison between BRAF and NRAS mutant versus wild type samples identified mostly constituents or regulators of MAPK and related pathways. When testing gene lists discriminative of BRAF, NRAS and MAPK alterations, we found that 112 BRAF‐specific transcripts were able to distinguish the two immune‐related phenotypes already described in melanoma, with the poor phenotype associated mostly with BRAF mutation. Noteworthy, such association was stronger in samples displaying low BRAF mRNA expression. However, when testing NRAS mutations, we were not able to find the same association. Conclusion This study suggests that BRAF mutation‐related specific transcripts associate with a poor phenotype in melanoma and provide a nest for further investigation. BRAF and NRAS status was assessed in 113 melanoma metastases by Sanger sequencing and high sensitive allele‐specific PCR. The expression of BRAF‐specific genes categorized the metastases in two divergent groups. The mutant group associated with a poor phenotype. The association between BRAF mutation and the poor phenotype was stronger in samples displaying low BRAF mRNA expression. Functional interpretation of BRAF expression‐discriminative genes revealed pathways related to an unfavorable phenotype.
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Affiliation(s)
- Sara Tomei
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Department of Genetic Medicine, Weill Cornell Medical College in Qatar, PO Box 24144, Doha, Qatar; Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar.
| | - Davide Bedognetti
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar
| | - Valeria De Giorgi
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Michele Sommariva
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
| | - Sara Civini
- Cell Processing Section, Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Reinboth
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg 97074, Germany; Genelux Corporation, San Diego Science Center, San Diego 92109, USA
| | - Muna Al Hashmi
- Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar
| | - Maria Libera Ascierto
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Center of Excellence for Biomedical Research (CEBR), University of Genoa, Italy
| | - Qiuzhen Liu
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Ben D Ayotte
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Andrea Worschech
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, PO Box 24144, Doha, Qatar
| | - Lorenzo Uccellini
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Institute of Infectious and Tropical Diseases, University of Milan, L. Sacco Hospital, Milan, Italy
| | - Paolo A Ascierto
- Istituto Nazionale Tumori Fondazione "G. Pascale", Via G. Semmola, Naples, Italy
| | - David Stroncek
- Cell Processing Section, Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
| | - Giuseppe Palmieri
- Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, PO Box 24144, Doha, Qatar
| | - Ena Wang
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar
| | - Francesco M Marincola
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA; Sidra Medical and Research Center, P.O. Box 26999, Doha, Qatar
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143
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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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144
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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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145
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Primary melanoma tumors from CDKN2A mutation carriers do not belong to a distinct molecular subclass. J Invest Dermatol 2014; 134:3000-3003. [PMID: 24999598 DOI: 10.1038/jid.2014.272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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146
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Ratzinger G, Mitteregger S, Wolf B, Berger R, Zelger B, Weinlich G, Fritsch P, Goebel G, Fiegl H. Association of TNFRSF10D DNA-methylation with the survival of melanoma patients. Int J Mol Sci 2014; 15:11984-95. [PMID: 25003639 PMCID: PMC4139825 DOI: 10.3390/ijms150711984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 12/31/2022] Open
Abstract
In this retrospective pilot study, the DNA-methylation status of genes that have been demonstrated to be involved in melanoma carcinogenesis was analyzed in order to identify novel biomarkers for the risk assessment of melanoma patients. We analyzed DNA extracted from punch-biopsies from 68 formalin-fixed paraffin-embedded (FFPE) melanoma specimens. Using MethyLight PCR, we examined 20 genes in specimens from a training set comprising 36 melanoma patients. Selected candidate genes were validated in a test set using FFPE tissue samples from 32 melanoma patients. First, we identified the TNFRSF10D DNA-methylation status (TNFRSF10D methylated vs. unmethylated) as a prognostic marker for overall (p = 0.001) and for relapse-free survival (p = 0.008) in the training set. This finding was confirmed in the independent test set (n = 32; overall survival p = 0.041; relapse-free survival p = 0.012). In a multivariate Cox-regression analysis including all patients, the TNFRSF10D DNA-methylation status remained as the most significant prognostic parameter for overall and relapse-free survival (relative-risk (RR) of death, 4.6 (95% CI: 2.0–11.0; p < 0.001), RR of relapse, 7.2 (95% CI: 2.8–18.3; p < 0.001)). In this study, we demonstrate that TNFRSF10D DNA-methylation analysis of a small tissue-punch from archival FFPE melanoma tissue is a promising approach to provide prognostic information in patients with melanoma.
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Affiliation(s)
- Gudrun Ratzinger
- Department of Dermatology and Venereology, Innsbruck Medical University, Innsbruck 6020, Austria.
| | - Simone Mitteregger
- Department of Dermatology and Venereology, Innsbruck Medical University, Innsbruck 6020, Austria.
| | - Barbara Wolf
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck 6020, Austria.
| | - Regina Berger
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck 6020, Austria.
| | - Bernhard Zelger
- Department of Dermatology and Venereology, Innsbruck Medical University, Innsbruck 6020, Austria.
| | - Georg Weinlich
- Department of Dermatology and Venereology, Innsbruck Medical University, Innsbruck 6020, Austria.
| | - Peter Fritsch
- Department of Dermatology and Venereology, Innsbruck Medical University, Innsbruck 6020, Austria.
| | - Georg Goebel
- Department of Medical Statistics, Informatics and Health Economics, Innsbruck Medical University, Innsbruck 6020, Austria.
| | - Heidelinde Fiegl
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck 6020, Austria.
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147
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Pitzalis C, Jones GW, Bombardieri M, Jones SA. Ectopic lymphoid-like structures in infection, cancer and autoimmunity. Nat Rev Immunol 2014; 14:447-62. [PMID: 24948366 DOI: 10.1038/nri3700] [Citation(s) in RCA: 472] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ectopic lymphoid-like structures often develop at sites of inflammation where they influence the course of infection, autoimmune disease, cancer and transplant rejection. These lymphoid aggregates range from tight clusters of B cells and T cells to highly organized structures that comprise functional germinal centres. Although the mechanisms governing ectopic lymphoid neogenesis in human pathology remain poorly defined, the presence of ectopic lymphoid-like structures within inflamed tissues has been linked to both protective and deleterious outcomes in patients. In this Review, we discuss investigations in both experimental model systems and patient cohorts to provide a perspective on the formation and functions of ectopic lymphoid-like structures in human pathology, with particular reference to the clinical implications and the potential for therapeutic targeting.
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Affiliation(s)
- Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Gareth W Jones
- Cardiff Institute for Infection and Immunity, The School of Medicine, Cardiff University, The Tenovus Building, Heath Campus, Cardiff CF14 4XN, Wales, UK
| | - Michele Bombardieri
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London, School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Simon A Jones
- Cardiff Institute for Infection and Immunity, The School of Medicine, Cardiff University, The Tenovus Building, Heath Campus, Cardiff CF14 4XN, Wales, UK
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148
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Neagu M, Constantin C. Highlights from the field of biomarkers in melanoma. Biomark Med 2014. [DOI: 10.2217/bmm.14.43] [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
Affiliation(s)
- Monica Neagu
- ‘Victor Babes’ National Institute of Pathology, 99-101 Splaiul Independentei, Bucharest 050096, Romania
| | - Carolina Constantin
- ‘Victor Babes’ National Institute of Pathology, 99-101 Splaiul Independentei, Bucharest 050096, Romania
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149
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Pimenta EM, Barnes BJ. Role of Tertiary Lymphoid Structures (TLS) in Anti-Tumor Immunity: Potential Tumor-Induced Cytokines/Chemokines that Regulate TLS Formation in Epithelial-Derived Cancers. Cancers (Basel) 2014; 6:969-97. [PMID: 24762633 PMCID: PMC4074812 DOI: 10.3390/cancers6020969] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/19/2014] [Accepted: 03/31/2014] [Indexed: 12/12/2022] Open
Abstract
Following the successes of monoclonal antibody immunotherapies (trastuzumab (Herceptin®) and rituximab (Rituxan®)) and the first approved cancer vaccine, Provenge® (sipuleucel-T), investigations into the immune system and how it can be modified by a tumor has become an exciting and promising new field of cancer research. Dozens of clinical trials for new antibodies, cancer and adjuvant vaccines, and autologous T and dendritic cell transfers are ongoing in hopes of identifying ways to re-awaken the immune system and force an anti-tumor response. To date, however, few consistent, reproducible, or clinically-relevant effects have been shown using vaccine or autologous cell transfers due in part to the fact that the immunosuppressive mechanisms of the tumor have not been overcome. Much of the research focus has been on re-activating or priming cytotoxic T cells to recognize tumor, in some cases completely disregarding the potential roles that B cells play in immune surveillance or how a solid tumor should be treated to maximize immunogenicity. Here, we will summarize what is currently known about the induction or evasion of humoral immunity via tumor-induced cytokine/chemokine expression and how formation of tertiary lymphoid structures (TLS) within the tumor microenvironment may be used to enhance immunotherapy response.
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Affiliation(s)
- Erica M Pimenta
- Rutgers Biomedical and Health Sciences, New Jersey Medical School-Cancer Center, Newark, NJ 07103, USA.
| | - Betsy J Barnes
- Department of Biochemistry and Molecular Biology, Rutgers Biomedical and Health Sciences, New Jersey Medical School-Cancer Center, Newark, NJ 07103, USA.
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150
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Molecular pathology of malignant melanoma: changing the clinical practice paradigm toward a personalized approach. Hum Pathol 2014; 45:1315-26. [PMID: 24856851 DOI: 10.1016/j.humpath.2014.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/04/2014] [Accepted: 04/09/2014] [Indexed: 12/14/2022]
Abstract
Melanocytic proliferations are notoriously difficult lesions to evaluate histologically, even among experts, as there is a lack of objective, highly reproducible criteria, which can be broadly applied to the wide range of melanocytic lesions encountered in daily practice. These difficult diagnoses are undeniably further compounded by the substantial medicolegal risks of an "erroneous" diagnosis. Molecular information and classification of melanocytic lesions is already vast and constantly expanding. The application of molecular techniques for the diagnosis of benignity or malignancy is, at times, confusing and limits its utility if not used properly. In addition, current and future therapies will necessitate molecular classification of melanoma into one of several distinct subtypes for appropriate patient-specific therapy. An understanding of what different molecular markers can and cannot predict is of the utmost importance. We discuss both mutational analysis and chromosomal gains/losses to help clarify this continually developing and confusing facet of pathology.
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