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Chan WH, Tsao H. Consensus, Controversy, and Conversations About Gene Expression Profiling in Melanoma. JAMA Dermatol 2021; 156:949-951. [PMID: 32745178 DOI: 10.1001/jamadermatol.2020.1730] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Warren H Chan
- Department of Dermatology, Stanford University School of Medicine, Stanford, California.,Department of Medicine, School of Medicine, Baylor College of Medicine, Houston, Texas
| | - Hensin Tsao
- Wellman Center for Photomedicine, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston
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2
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Lee S, Suh HB, Choi SJ, Kang J, Kang JW, Kwon EJ, Kim HJ, Kim YH, Shin K. Identification of prognostic mRNAs in metastatic cutaneous melanoma. Melanoma Res 2020; 30:543-547. [PMID: 33003118 DOI: 10.1097/cmr.0000000000000697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cutaneous melanoma is the most common cause of skin cancer-related deaths worldwide. There is an urgent need to identify prognostic biomarkers to facilitate decision-making for treatment of metastatic cutaneous melanoma. Gene expression microarrays and RNA-seq technology have recently improved or changed current prognostic and therapeutic strategies for several cancers. However, according to the current melanoma staging system, prognosis is almost entirely dependent on clinicopathological features. To identify novel prognostic biomarkers, we investigated gene expression and clinical data for patients with cutaneous melanoma from three cohorts of The Cancer Genome Atlas and Gene Expression Omnibus. Kaplan-Meier survival analysis using median values of each gene as cutoff value revealed that nine genes (ABCC3, CAPS2, CCR6, CDCA8, CLU, DPF1, PTK2B, SATB1, and SYNE1) were statistically significant prognostic biomarkers of metastatic cutaneous melanoma in all three independent cohorts. Low expression of two genes (CDCA8 and DPF1) and high expression of seven genes (ABCC3, CAPS2, CCR6, CLU, PTK2B, SATB1, and SYNE) were significantly associated with positive metastatic cutaneous melanoma prognoses. In conclusion, we suggest nine novel prognostic biomarkers for cutaneous metastatic melanoma.
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Affiliation(s)
| | - Hie Bum Suh
- Department of Radiology, School of Medicine, Pusan National University
- Biomedical Research Institute, Pusan National University Hospital
| | | | | | | | | | | | - Yun Hak Kim
- Department of Biomedical Informatics
- Department of Anatomy, School of Medicine, Pusan National University
| | - Kihyuk Shin
- Biomedical Research Institute, Pusan National University Hospital
- Department of Dermatology
- Department of Dermatology, Pusan National University Yangsan Hospital
- Research Institute for Convergence of Biomedical Science and Technology, Yangsan, Korea
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3
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Xiong J, Su Y, Bing Z, Zhao B. Survival between synchronous and non-synchronous multiple primary cutaneous melanomas-a SEER database analysis. PeerJ 2020; 8:e8316. [PMID: 31915586 PMCID: PMC6944097 DOI: 10.7717/peerj.8316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/29/2019] [Indexed: 12/14/2022] Open
Abstract
Background There is no criterion to distinguish synchronous and non-synchronous multiple primary cutaneous melanomas (MPMs). This study aimed to distinguish synchronous and non-synchronous MPMs and compare the survivals of them using the Surveillance, Epidemiology, and End Results database. Methods Synchronous and non-synchronous MPMs were distinguished by fitting the double log transformed distribution of the time interval between the first and second primary cutaneous melanomas (TIFtS) through a piecewise linear regression. The overall and melanoma-specific survivals were compared by the Kaplan-Meier method and Cox proportional hazard model through modeling the occurrence of synchronous MPMs as a time-dependent variable. Results The distribution of TIFtS was composed by three power-law distributions. According to its first inflection point, synchronous MPMs were defined as tumors that occurred within 2 months. The Kaplain-Meier plot revealed a significant inferior survival for synchronous MPMs than non-synchronous MPMs (P < 0.0001), and the occurrence of synchronous MPM was a risk factor for overall survival of cutaneous melanoma (CM) (hazard ratio: 2.213; (95% CI [2.087-2.346]); P < 0.0001). Conclusions This study provided data analysis evidences for using 2 months to distinguish synchronous MPMs and non-synchronous MPMs. Furthermore, the occurrence of synchronous MPM was a risk factor for prognosis of patients with CM.
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Affiliation(s)
- Jie Xiong
- Department of Mathematics and Computer Science, Changsha University, Changsha, Hunan, China.,Department of Epidemiology and Health Statistics, Central South University, Changsha, Hunan, China
| | - Yanlin Su
- Department of Gynaecology and Obstetrics, Changsha Central Hospital, Changsha, Hunan, China
| | - Zhitong Bing
- Evidence Based Medicine Center, Lanzhou University, Lanzhou, Gansu, China
| | - Bihai Zhao
- Department of Mathematics and Computer Science, Changsha University, Changsha, Hunan, China
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4
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Min KW, Choe JY, Kwon MJ, Lee HK, Kang HS, Nam ES, Cho SJ, Park HR, Min SK, Seo J, Kim YJ, Kim NY, Kim HY. BRAF and NRAS mutations and antitumor immunity in Korean malignant melanomas and their prognostic relevance: Gene set enrichment analysis and CIBERSORT analysis. Pathol Res Pract 2019; 215:152671. [DOI: 10.1016/j.prp.2019.152671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
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5
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Cho SI, Lee J, Jo G, Kim SW, Minn KW, Hong KY, Jo SJ, Cho KH, Kim BJ, Mun JH. Local recurrence and metastasis in patients with malignant melanomas after surgery: A single-center analysis of 202 patients in South Korea. PLoS One 2019; 14:e0213475. [PMID: 30845184 PMCID: PMC6405088 DOI: 10.1371/journal.pone.0213475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/21/2019] [Indexed: 11/22/2022] Open
Abstract
Malignant melanoma (MM) is a lethal skin cancer in Western countries. Although the incidence is low in Asians compared to that in Caucasians, it is increasing. However, literature regarding risk factors for prognosis of MM patients who have undergone surgical excision in Asian is limited. This study aimed to investigate the predictive factors for local recurrence and metastasis in MM patients who underwent surgical treatment at a single tertiary-level hospital in Korea. Patients who underwent surgery for MM at our institution between January 1998 and December 2014 were analyzed. We retrospectively investigated risk factors for local recurrence and metastasis after surgery. In cases with distant metastasis, tumor thickness (adjusted Hazard Ratio (HR), 6.139; 95% confidence interval (CI), 2.152 to 17.509; P = 0.001) and increased mitotic number [(0-1/mm2 vs 2-6/mm2: adjusted HR, 4.483; 95% CI, 1.233 to 16.303; P = 0.023); (0-1/mm2 vs > 6/mm2: adjusted HR, 10.316; 95% CI, 2.871 to 37.063; P < 0.001)] were associated with risk in multivariate analysis. Regarding local recurrence, tumor thickness (T4 [≥4mm] vs T1) was found to be a significant risk factor (adjusted HR, 8.461; 95% CI, 2.514 to 28.474; P = 0.001). Our data revealed tumor thickness and increased mitotic count were significant risk factors for local recurrence and distant metastasis in Korean patients with MM after surgery.
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Affiliation(s)
- Soo Ick Cho
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - Jaewon Lee
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - Gwanghyun Jo
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - Sang Wha Kim
- Department of Plastic and Reconstructive Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyung Won Minn
- Department of Plastic and Reconstructive Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Ki Yong Hong
- Department of Plastic and Reconstructive Surgery, Dongguk University Ilsan Hospital, Goyang, South Korea
| | - Seong Jin Jo
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - Kwang Hyun Cho
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - Byung Jun Kim
- Department of Plastic and Reconstructive Surgery, Seoul National University College of Medicine, Seoul, South Korea
- * E-mail: (JHM); (BJK)
| | - Je-Ho Mun
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
- * E-mail: (JHM); (BJK)
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6
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Surowy HM, Giesen AK, Otte J, Büttner R, Falkenstein D, Friedl H, Meier F, Petzsch P, Wachtmeister T, Westphal D, Wieczorek D, Wruck W, Adjaye J, Rütten A, Redler S. Gene expression profiling in aggressive digital papillary adenocarcinoma sheds light on the architecture of a rare sweat gland carcinoma. Br J Dermatol 2019; 180:1150-1160. [PMID: 30472730 DOI: 10.1111/bjd.17446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Sweat gland carcinomas are rare cutaneous adnexal malignancies. Aggressive digital papillary adenocarcinoma (ADPA) represents a very rare subentity, thought to arise almost exclusively from the sweat glands of the fingers and toes. The aetiology of sweat gland carcinomas and ADPA is largely unknown. ADPAs are most likely driven by somatic mutations. However, somatic mutation patterns are largely unexplored, creating barriers to the development of effective therapeutic approaches to the treatment of ADPA. OBJECTIVES To investigate the transcriptome profile of ADPA using a sample of eight formalin-fixed, paraffin-embedded tissue samples of ADPA and healthy control tissue. METHODS Transcriptome profiling was performed using the Affymetrix PrimeView Human Gene Expression Microarray and findings were validated via reverse transcription of RNA and real-time quantitative polymerase chain reaction. RESULTS Transcriptome analyses showed increased tumour expression of 2266 genes, with significant involvement of cell cycle, ribosomal and crucial cancer pathways. Our results point to tumour overexpression of FGFR2 (P = 0·001). CONCLUSIONS The results indicate the involvement of crucial oncogenic driver pathways, highlighting cell cycle and ribosomal pathways in the aetiology of ADPA. Suggested tumour overexpression of FGFR2 raises the hope that targeting the fibroblast growth factor (FGF)/FGF receptor axis might be a promising treatment for ADPA and probably for the overall group of sweat gland carcinomas.
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Affiliation(s)
- H M Surowy
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
| | - A K Giesen
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
| | - J Otte
- Institute for Stem Cell Research and Regenerative Medicine, Düsseldorf, Germany
| | - R Büttner
- Pathology, Institute for Pathology, University Hospital Cologne, Cologne, Germany
| | - D Falkenstein
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
| | - H Friedl
- Klinikum Darmstadt, Department of Dermatology, Darmstadt, Germany
| | - F Meier
- Department of Dermatology, Carl Gustav Carus Medical Center, TU Dresden, Dresden, Germany.,National Center for Tumour Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - P Petzsch
- Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - T Wachtmeister
- Biological and Medical Research Center (BMFZ), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - D Westphal
- Department of Dermatology, Carl Gustav Carus Medical Center, TU Dresden, Dresden, Germany.,National Center for Tumour Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - D Wieczorek
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
| | - W Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Düsseldorf, Germany
| | - J Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Düsseldorf, Germany
| | - A Rütten
- Dermatopathology, Bodensee, Siemensstrasse 6/1, 88048, Friedrichshafen, Germany
| | - S Redler
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Düsseldorf, Germany
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7
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Swetter SM, Tsao H, Bichakjian CK, Curiel-Lewandrowski C, Elder DE, Gershenwald JE, Guild V, Grant-Kels JM, Halpern AC, Johnson TM, Sober AJ, Thompson JA, Wisco OJ, Wyatt S, Hu S, Lamina T. Guidelines of care for the management of primary cutaneous melanoma. J Am Acad Dermatol 2018; 80:208-250. [PMID: 30392755 DOI: 10.1016/j.jaad.2018.08.055] [Citation(s) in RCA: 328] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022]
Abstract
The incidence of primary cutaneous melanoma continues to increase each year. Melanoma accounts for the majority of skin cancer-related deaths, but treatment is usually curative following early detection of disease. In this American Academy of Dermatology clinical practice guideline, updated treatment recommendations are provided for patients with primary cutaneous melanoma (American Joint Committee on Cancer stages 0-IIC and pathologic stage III by virtue of a positive sentinel lymph node biopsy). Biopsy techniques for a lesion that is clinically suggestive of melanoma are reviewed, as are recommendations for the histopathologic interpretation of cutaneous melanoma. The use of laboratory, molecular, and imaging tests is examined in the initial work-up of patients with newly diagnosed melanoma and for follow-up of asymptomatic patients. With regard to treatment of primary cutaneous melanoma, recommendations for surgical margins and the concepts of staged excision (including Mohs micrographic surgery) and nonsurgical treatments for melanoma in situ, lentigo maligna type (including topical imiquimod and radiation therapy), are updated. The role of sentinel lymph node biopsy as a staging technique for cutaneous melanoma is described, with recommendations for its use in clinical practice. Finally, current data regarding pregnancy and melanoma, genetic testing for familial melanoma, and management of dermatologic toxicities related to novel targeted agents and immunotherapies for patients with advanced disease are summarized.
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Affiliation(s)
- Susan M Swetter
- Department of Dermatology, Stanford University Medical Center and Cancer Institute, Stanford, California; Veterans Affairs Palo Alto Health Care System, Palo Alto, California.
| | - Hensin Tsao
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Wellman Center for Photomedicine, Boston, Massachusetts
| | - Christopher K Bichakjian
- Department of Dermatology, University of Michigan Health System, Ann Arbor, Michigan; Comprehensive Cancer Center, Ann Arbor, Michigan
| | - Clara Curiel-Lewandrowski
- Division of Dermatology, University of Arizona, Tucson, Arizona; University of Arizona Cancer Center, Tucson, Arizona
| | - David E Elder
- Department of Dermatology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania; Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas; Department of Cancer Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Jane M Grant-Kels
- Department of Dermatology, University of Connecticut Health Center, Farmington, Connecticut; Department of Pathology, University of Connecticut Health Center, Farmington, Connecticut; Department of Pediatrics, University of Connecticut Health Center, Farmington, Connecticut
| | - Allan C Halpern
- Department of Dermatology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Timothy M Johnson
- Department of Dermatology, University of Michigan Health System, Ann Arbor, Michigan; Comprehensive Cancer Center, Ann Arbor, Michigan
| | - Arthur J Sober
- Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - John A Thompson
- Division of Oncology, University of Washington, Seattle, Washington; Seattle Cancer Care Alliance, Seattle, Washington
| | - Oliver J Wisco
- Department of Dermatology, Oregon Health and Science University, Portland, Oregon
| | | | - Shasa Hu
- Department of Dermatology, University of Miami Health System, Miami, Florida
| | - Toyin Lamina
- American Academy of Dermatology, Rosemont, Illinois
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8
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Abstract
A large variety of molecular pathways in melanoma progression suggests that no individual molecular alteration is crucial in itself. Our aim was to define the molecular alterations underlying metastasis formation. Gene expression profiling was performed using microarray and qRT-PCR to define alterations between matched primary and metastatic melanoma cell lines. These data were integrated with publicly available unmatched tissue data. The invasiveness of cell lines was determined by Matrigel invasion assays and invasive clones from primary melanoma-derived cell lines were also selected. Two metastatic cell line models were created: the regional lymph node WM983A-WM983A-WM983B and the distant lung WM793B-WM793B-1205Lu metastatic models. The majority of metastasis genes were downregulated and enriched in adhesion and ITGA6-B4 pathways. Upregulation of immune pathways was characteristic of distant metastases, whereas increased Rap1 signaling was specific for regional (sub)cutaneous metastases. qRT-PCR analysis of selected integrins (A2, A3, A4, A9, B5, B8, A6, B1, and B3) highlighted the possible importance of ITGA3/4 and B8 in the metastatic process, distinguishing regional and distant metastases. We identified functionally relevant gene clusters that influenced metastasis formation. Our data provide further evidence that integrin expression patterns may be important in distant metastasis formation.
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9
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Lardone RD, Plaisier SB, Navarrete MS, Shamonki JM, Jalas JR, Sieling PA, Lee DJ. Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma. Oncotarget 2018; 7:14415-28. [PMID: 26883106 PMCID: PMC4924725 DOI: 10.18632/oncotarget.7361] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/29/2016] [Indexed: 12/11/2022] Open
Abstract
Platform and study differences in prognostic signatures from metastatic melanoma (MM) gene expression reports often hinder consensus arrival. We performed survival/outcome-based pairwise comparisons of three independent MM gene expression profiles using the threshold-free algorithm rank-rank hypergeometric overlap analysis (RRHO). We found statistically significant overlap for genes overexpressed in favorable outcome (FO) groups, but no overlap for poor outcome (PO) groups. This “favorable outcome signature” (FOS) of 228 genes coinciding on all three overlapping gene lists showed immune function predominated in FO MM. Surprisingly, specific cell signature-enrichment analysis showed B cell-associated genes enriched in FO MM, along with T cell-associated genes. Higher levels of B and T cells (p<0.05) and their relative proximity (p<0.05) were detected in FO-to-PO tumor comparisons from an independent MM patients cohort. Finally, expression of FOS in two independent Stage III MM tumor datasets correctly predicted clinical outcome in 12/14 and 44/70 patients using a weighted gene voting classifier (area under the curve values 0.96 and 0.75, respectively). This RRHO-based, cross-study analysis emphasizes the RRHO approach power, confirms T cells relevance for prolonged MM survival, supports a favorable role for B cells in anti-melanoma immunity, and suggests B cells potential as means of intervention in melanoma treatment.
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Affiliation(s)
- Ricardo D Lardone
- Department of Translational Immunology, Dirks/Dougherty Laboratory for Cancer Research, John Wayne Cancer Institute, Santa Monica, CA 90404, USA
| | - Seema B Plaisier
- Department of Translational Immunology, Dirks/Dougherty Laboratory for Cancer Research, John Wayne Cancer Institute, Santa Monica, CA 90404, USA
| | - Marian S Navarrete
- Department of Translational Immunology, Dirks/Dougherty Laboratory for Cancer Research, John Wayne Cancer Institute, Santa Monica, CA 90404, USA
| | | | - John R Jalas
- Department of Pathology at Providence Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Peter A Sieling
- Department of Translational Immunology, Dirks/Dougherty Laboratory for Cancer Research, John Wayne Cancer Institute, Santa Monica, CA 90404, USA
| | - Delphine J Lee
- Department of Translational Immunology, Dirks/Dougherty Laboratory for Cancer Research, John Wayne Cancer Institute, Santa Monica, CA 90404, USA
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Rodríguez-Cerdeira C, Molares-Vila A, Carnero-Gregorio M, Corbalán-Rivas A. Recent advances in melanoma research via "omics" platforms. J Proteomics 2017; 188:152-166. [PMID: 29138111 DOI: 10.1016/j.jprot.2017.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/25/2017] [Accepted: 11/08/2017] [Indexed: 02/09/2023]
Abstract
Melanoma has a high mortality rate and metastatic melanoma is highly resistant to conventional therapies. "Omics" fields such as proteomics and microRNA and exosome studies have provided new knowledge to complement the information generated by genomic studies. This work aimed to review the current status of biomarker discovery for melanoma through multi-"omics" platforms. A few sets of novel microRNAs and proteins are described, some of them with important implications in suppressing melanoma at different stages. Upregulation of genes involved in angiogenesis, immunosuppressive factors, modification of stroma, capture of melanoma cells in lymph nodes and factors responsible for tumour cell recruitment have been identified in exosomes, among molecules with other functions. A remarkable series of proteins involved in epithelial-mesenchymal/mesenchymal-epithelial transitions, inflammation, motility, proliferation and progression processes, centrosome amplification, aneuploidy, inhibition of CD8+ effector T-cells, and metastasis in general were identified. Genomic and protein-protein interactions or metabolome levels were not analysed. Proteomics tools such as Orbitrap shotgun mass spectrometry or deep mining proteomic analysis utilizing high-resolution reversed phase nanoseparation in combination with mass spectrometry are also discussed. The application of these tools together with bioinformatics approaches applied to the clinical setting will enable the implementation of personalized medicine in the near future.
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Affiliation(s)
- Carmen Rodríguez-Cerdeira
- Efficiency, Quality and Costs in Health Services Research Group (EFISALUD), Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain; Dermatology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain.
| | - Alberto Molares-Vila
- Efficiency, Quality and Costs in Health Services Research Group (EFISALUD), Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain; Department of Analytical & Food Chemistry, Universidade de Vigo (UVIGO), Spain
| | - Miguel Carnero-Gregorio
- Efficiency, Quality and Costs in Health Services Research Group (EFISALUD), Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain; Department of Biochemistry, Genetics & Immunology, Universidade de Vigo (UVIGO), Spain
| | - Alberte Corbalán-Rivas
- Nursery Department, Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, A Coruña, Spain
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11
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Neubert NJ, Soneson C, Barras D, Baumgaertner P, Rimoldi D, Delorenzi M, Fuertes Marraco SA, Speiser DE. A Well-Controlled Experimental System to Study Interactions of Cytotoxic T Lymphocytes with Tumor Cells. Front Immunol 2016; 7:326. [PMID: 27625650 PMCID: PMC5003846 DOI: 10.3389/fimmu.2016.00326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/15/2016] [Indexed: 11/13/2022] Open
Abstract
While T cell-based immunotherapies are steadily improving, there are still many patients who progress, despite T cell-infiltrated tumors. Emerging evidence suggests that T cells themselves may provoke immune escape of cancer cells. Here, we describe a well-controlled co-culture system for studying the dynamic T cell - cancer cell interplay, using human melanoma as a model. We explain starting material, controls, and culture parameters to establish reproducible and comparable cultures with highly heterogeneous tumor cells. Low passage melanoma cell lines and melanoma-specific CD8+ T cell clones generated from patient blood were cultured together for up to 3 days. Living melanoma cells were isolated from the co-culture system by fluorescence-activated cell sorting. We demonstrate that the characterization of isolated melanoma cells is feasible using flow cytometry for protein expression analysis as well as an Agilent whole human genome microarray and the NanoString technology for differential gene expression analysis. In addition, we identify five genes (ALG12, GUSB, RPLP0, KRBA2, and ADAT2) that are stably expressed in melanoma cells independent of the presence of T cells or the T cell-derived cytokines IFNγ and TNFα. These genes are essential for correct normalization of gene expression data by NanoString. Further to the characterization of melanoma cells after exposure to CTLs, this experimental system might be suitable to answer a series of questions, including how the affinity of CTLs for their target antigen influences the melanoma cell response and whether CTL-induced gene expression changes in melanoma cells are reversible. Taken together, our human T cell - melanoma cell culture system is well suited to characterize immune-related mechanisms in cancer cells.
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Affiliation(s)
- Natalie J Neubert
- Department of Oncology, Ludwig Center for Cancer Research, University of Lausanne , Epalinges , Switzerland
| | - Charlotte Soneson
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics , Lausanne , Switzerland
| | - David Barras
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics , Lausanne , Switzerland
| | - Petra Baumgaertner
- Department of Oncology, Ludwig Center for Cancer Research, University of Lausanne , Epalinges , Switzerland
| | - Donata Rimoldi
- Department of Oncology, Ludwig Center for Cancer Research, University of Lausanne , Epalinges , Switzerland
| | - Mauro Delorenzi
- Department of Oncology, Ludwig Center for Cancer Research, University of Lausanne, Epalinges, Switzerland; Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Silvia A Fuertes Marraco
- Department of Oncology, Ludwig Center for Cancer Research, University of Lausanne , Epalinges , Switzerland
| | - Daniel E Speiser
- Department of Oncology, Ludwig Center for Cancer Research, University of Lausanne , Epalinges , Switzerland
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12
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Rowe CJ, Khosrotehrani K. Clinical and biological determinants of melanoma progression: Should all be considered for clinical management? Australas J Dermatol 2016; 57:175-81. [PMID: 26010424 DOI: 10.1111/ajd.12348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/05/2015] [Indexed: 01/30/2023]
Abstract
Cutaneous melanoma is a heterogeneous disease affecting the regulation of multiple genes and proteins that contribute to melanoma progression. Survival for patients with locally invasive disease varies greatly, even within tumour stages based on current prognostic criteria. This has prompted investigations into the value of additional clinical or biological parameters predicting survival. In particular, the improved knowledge of tumour biology has fed the hope that the outcome may be predicted at the molecular level. The prognostic value of numerous potential biomarkers has therefore been evaluated in protein and gene expression studies, and genomic associations with melanoma prognosis are beginning to emerge. These potential biomarkers interrogate key tumour and host processes important for tumour development and progression, such as proliferation, invasion and migration through epithelial mesenchymal transition or the host immune or vascular responses. This research may allow more individualised information on prognosis if the challenges regarding the quality and validation of studies are overcome.
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Affiliation(s)
- Casey J Rowe
- Translational Research Institute, UQ Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia
- University of Queensland Centre for Clinical Research, University of Queensland, Herston, Queensland, Australia
| | - Kiarash Khosrotehrani
- Translational Research Institute, UQ Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia
- University of Queensland Centre for Clinical Research, University of Queensland, Herston, Queensland, Australia
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13
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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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14
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Identification, Review, and Systematic Cross-Validation of microRNA Prognostic Signatures in Metastatic Melanoma. J Invest Dermatol 2016; 136:245-254. [PMID: 26763444 DOI: 10.1038/jid.2015.355] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 08/06/2015] [Accepted: 08/17/2015] [Indexed: 01/14/2023]
Abstract
In metastatic melanoma, it is vital to identify and validate biomarkers of prognosis. Previous studies have systematically evaluated protein biomarkers or mRNA-based expression signatures. No such analyses have been applied to microRNA (miRNA)-based prognostic signatures. As a first step, we identified two prognostic miRNA signatures from publicly available data sets (Gene Expression Omnibus/The Cancer Genome Atlas) of global miRNA expression profiling information. A 12-miRNA signature predicted longer survival after surgery for resection of American Joint Committee on Cancer stage III disease (>4 years, no sign of relapse) and outperformed American Joint Committee on Cancer standard-of-care prognostic markers in leave-one-out cross-validation analysis (error rates 34% and 38%, respectively). A similar 15-miRNA biomarker derived from The Cancer Genome Atlas miRNA-seq data performed slightly worse (39%) than these current biomarkers. Both signatures were then assessed for replication in two independent data sets and subjected to systematic cross-validation together with the three other miRNA-based prognostic signatures proposed in the literature to date. Five miRNAs (miR-142-5p, miR-150-5p, miR-342-3p, miR-155-5p, and miR-146b-5p) were reproducibly associated with patient outcome and have the greatest potential for application in the clinic. Our extensive validation approach highlighted among multiple independent cohorts the translational potential and limitations of miRNA signatures, and pointed to future directions in the analysis of this emerging class of markers.
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15
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Rowe CJ, Tang F, Hughes MCB, Rodero MP, Malt M, Lambie D, Barbour A, Hayward NK, Smithers BM, Green AC, Khosrotehrani K. Molecular markers to complement sentinel node status in predicting survival in patients with high-risk locally invasive melanoma. Int J Cancer 2016; 139:664-72. [PMID: 26990817 DOI: 10.1002/ijc.30085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/08/2016] [Accepted: 02/29/2016] [Indexed: 11/11/2022]
Abstract
Sentinel lymph node status is a major prognostic marker in locally invasive cutaneous melanoma. However, this procedure is not always feasible, requires advanced logistics and carries rare but significant morbidity. Previous studies have linked markers of tumour biology to patient survival. In this study, we aimed to combine the predictive value of established biomarkers in addition to clinical parameters as indicators of survival in addition to or instead of sentinel node biopsy in a cohort of high-risk melanoma patients. Patients with locally invasive melanomas undergoing sentinel lymph node biopsy were ascertained and prospectively followed. Information on mortality was validated through the National Death Index. Immunohistochemistry was used to analyse proteins previously reported to be associated with melanoma survival, namely Ki67, p16 and CD163. Evaluation and multivariate analyses according to REMARK criteria were used to generate models to predict disease-free and melanoma-specific survival. A total of 189 patients with available archival material of their primary tumour were analysed. Our study sample was representative of the entire cohort (N = 559). Average Breslow thickness was 2.5 mm. Thirty-two (17%) patients in the study sample died from melanoma during the follow-up period. A prognostic score was developed and was strongly predictive of survival, independent of sentinel node status. The score allowed classification of risk of melanoma death in sentinel node-negative patients. Combining clinicopathological factors and established biomarkers allows prediction of outcome in locally invasive melanoma and might be implemented in addition to or in cases when sentinel node biopsy cannot be performed.
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Affiliation(s)
- Casey J Rowe
- The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD, Australia.,The University of Queensland Centre for Clinical Research, Brisbane, QLD, Australia
| | - Fiona Tang
- Department of Anatomical Pathology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Maria Celia B Hughes
- Cancer and Population Studies, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Mathieu P Rodero
- The University of Queensland Centre for Clinical Research, Brisbane, QLD, Australia
| | - Maryrose Malt
- Cancer and Population Studies, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Duncan Lambie
- The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD, Australia.,IQ Pathology, West End, Brisbane, QLD, Australia
| | - Andrew Barbour
- Queensland Melanoma Project, Princess Alexandra Hospital, The University of Queensland, Brisbane, QLD, Australia
| | - Nicholas K Hayward
- Oncogenomics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - B Mark Smithers
- Queensland Melanoma Project, Princess Alexandra Hospital, The University of Queensland, Brisbane, QLD, Australia
| | - Adele C Green
- Cancer and Population Studies, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Cancer Research UK Manchester Institute and Institute of Inflammation and Repair, University of Manchester, Manchester, United Kingdom
| | - Kiarash Khosrotehrani
- The University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD, Australia.,The University of Queensland Centre for Clinical Research, Brisbane, QLD, Australia
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16
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Vogelsang M, Wilson M, Kirchhoff T. Germline determinants of clinical outcome of cutaneous melanoma. Pigment Cell Melanoma Res 2016; 29:15-26. [PMID: 26342156 PMCID: PMC5024571 DOI: 10.1111/pcmr.12418] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022]
Abstract
Cutaneous melanoma (CM) is the most lethal form of skin cancer. Despite the constant increase in melanoma incidence, which is in part due to incremental advances in early diagnostic modalities, mortality rates have not improved over the last decade and for advanced stages remain steadily high. While conventional prognostic biomarkers currently in use find significant utility for predicting overall general survival probabilities, they are not sensitive enough for a more personalized clinical assessment on an individual level. In recent years, the advent of genomic technologies has brought the promise of identification of germline DNA alterations that may associate with CM outcomes and hence represent novel biomarkers for clinical utilization. This review attempts to summarize the current state of knowledge of germline genetic factors studied for their impact on melanoma clinical outcomes. We also discuss ongoing problems and hurdles in validating such surrogates, and we also project future directions in discovery of more powerful germline genetic factors with clinical utility in melanoma prognostication.
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Affiliation(s)
- Matjaz Vogelsang
- Perlmutter Cancer Center, New York University School of Medicine, New York, USA
- Departments of Population Health and Environmental Medicine, New York University School of Medicine, New York, USA
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, USA
| | - Melissa Wilson
- Perlmutter Cancer Center, New York University School of Medicine, New York, USA
- Department of Medicine, New York University School of Medicine, New York, USA
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, USA
| | - Tomas Kirchhoff
- Perlmutter Cancer Center, New York University School of Medicine, New York, USA
- Departments of Population Health and Environmental Medicine, New York University School of Medicine, New York, USA
- The Interdisciplinary Melanoma Cooperative Group, New York University School of Medicine, New York, USA
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17
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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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18
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Pasquali S, Montesco MC, Ginanneschi C, Baroni G, Miracco C, Urso C, Mele F, Lombardi AR, Quaglino P, Cattaneo L, Staibano S, Botti G, Visca P, Zannoni M, Soda G, Corti B, Pilloni L, Anselmi L, Lissia A, Vannucchi M, Manieli C, Massi D. Lymphatic and blood vasculature in primary cutaneous melanomas of the scalp and neck. Head Neck 2015; 37:1596-602. [PMID: 24931916 DOI: 10.1002/hed.23801] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/12/2014] [Accepted: 06/11/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Scalp/neck melanomas have a poor prognosis, possibly because of a rich vascular supply that prompts tumor cells' dissemination. METHODS We compared the accuracy of immunohistochemical (IHC) staining with morphology for the identification of lymphovascular invasion in 156 scalp/neck melanomas. We then analyzed the association of vessel invasion and density with pathological features and survival. RESULTS IHC-detected lymphatic vessel invasion (LVI) and blood vessel invasion (BVI) were identified in 34.6% and 13.5% of cases, respectively. IHC increased the LVI/BVI detection compared to morphology (40.4% vs 16.6%; p < .001). The degree of peritumoral and intratumoral blood vessel density (BVD) was greater than lymphatic vessel density (LVD). Ulceration was the only factor independently associated with intratumoral (p = .029) and peritumoral (p = .047) BVD. Tumor thickness was the only independent predictor of survival (p = .002). CONCLUSION IHC allows accurate assessment of lymphovascular invasion in scalp/neck melanomas. In these tumors, we observed a high incidence of BVI, which deserves further investigations.
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Affiliation(s)
- Sandro Pasquali
- Melanoma and Sarcomas Unit, Veneto Institute of Oncology, Padova, Italy
| | | | | | | | | | | | - Fabio Mele
- "Di Venere" and "San Paolo" Hospital, Bari, Italy
| | | | | | | | | | | | - Paolo Visca
- National Cancer Institute "Regina Elena,", Roma, Italy
| | - Marina Zannoni
- Azienda Ospedaliero Universitaria Integrata Verona, Verona, Italy
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19
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Hersey P, Gowrishankar K. Pembrolizumab joins the anti-PD-1 armamentarium in the treatment of melanoma. Future Oncol 2015; 11:133-40. [PMID: 25572788 DOI: 10.2217/fon.14.205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pembrolizumab (MK-3475) is a monoclonal antibody that binds to the PD-1 receptor on T cells and prevents binding to its ligands PD-L1 and PD-L2. Blocking this receptor frees T cells from the inhibitory effects of PD-L1 and allows them to mediate antitumor effects against cancer cells. In a large Phase I study of 411 patients with melanoma, high durable response rates over a range of doses and schedules have been shown with very little toxicity. A Phase III study of pembrolizumab comparing two schedules of administration with the current standard treatment with the anti-CTLA-4 monoclonal antibody is in progress. Combinations with other checkpoint inhibitors as well as other anticancer agents are also being evaluated. Approval of pembrolizumab for the treatment of melanoma is expected.
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Affiliation(s)
- Peter Hersey
- Kolling Medical Research Institute, Royal North Shore Hospital, University of Sydney, St Leonards, NSW 2065, Australia
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20
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Sandro P, Andrea M, Nicola M, Simone M, Giuseppe M, Lorenzo B, Nicola S, Dario P, Luigi M, Giuseppe G, Roberto P, Corrado C, Simone R, Ugo M, Mario S, Riccardo RC. Lymph-Node Ratio in Patients with Cutaneous Melanoma: A Multi-Institution Prognostic Study. Ann Surg Oncol 2015; 22:2127-34. [PMID: 25316489 DOI: 10.1245/s10434-014-4132-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Indexed: 08/30/2023]
Abstract
BACKGROUND Lymph node ratio (LNR)-the number of metastatic lymph nodes (LNs) over the number of excised LNs after lymphadenectomy-is a prognostic factor for many solid tumors, but controversies still exist for skin melanoma. We investigated the prognostic relevance of LNR in melanoma patients and formulated a proposal for considering the LNR in the current American Joint Committee on Cancer (AJCC) N staging system. METHODS Retrospective data of 2,526 melanoma patients with LN metastasis from nine Italian institutions were collected in a multicenter database. The prognostic value of the LNR (categorized as A, ≤0.1; B, 0.11-0.25; and C, >0.25) was assessed by multivariable survival analysis. RESULTS LNR was a significant independent prognostic factor for melanoma-specific survival (LNR B vs. A: hazard ratio [HR] 1.47, 95 % CI 1.16-1.87, p = 0.002; LNR C vs. A: HR 1.84, 95 % CI 1.29-2.61, p = 0.001). The LNR had prognostic value in patients with AJCC N1a (one positive LN after sentinel LN biopsy [SLNB], HR 2.33, 95 % CI 1.49-3.63, p < 0.001) and N2a (two to three positive LNs after SLNB, HR 1.62, 95 % CI 1.09-2.40, p = 0.016) substages, but not in those with N1b (one clinically positive LN, p = 0.765), N2b (two to three clinically positive LNs, p = 0.165), and N3 (≥ four positive LNs, p = 0.084) substages. CONCLUSION The LNR is a prognostic factor in melanoma patients with one (AJCC N1a) and two to three (AJCC N2a) positive LNs after SLNB. This easy-to-obtain parameter should be considered for the staging of melanoma patients with LN metastasis, along with the number of positive LNs.
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Affiliation(s)
- Pasquali Sandro
- Surgery Branch, Department of Surgery Oncology and Gastroenterology, University of Padova, Padua, Italy
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21
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Li W, Freudenberg J, Oswald M. Principles for the organization of gene-sets. Comput Biol Chem 2015; 59 Pt B:139-49. [PMID: 26188561 DOI: 10.1016/j.compbiolchem.2015.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/08/2015] [Indexed: 12/23/2022]
Abstract
A gene-set, an important concept in microarray expression analysis and systems biology, is a collection of genes and/or their products (i.e. proteins) that have some features in common. There are many different ways to construct gene-sets, but a systematic organization of these ways is lacking. Gene-sets are mainly organized ad hoc in current public-domain databases, with group header names often determined by practical reasons (such as the types of technology in obtaining the gene-sets or a balanced number of gene-sets under a header). Here we aim at providing a gene-set organization principle according to the level at which genes are connected: homology, physical map proximity, chemical interaction, biological, and phenotypic-medical levels. We also distinguish two types of connections between genes: actual connection versus sharing of a label. Actual connections denote direct biological interactions, whereas shared label connection denotes shared membership in a group. Some extensions of the framework are also addressed such as overlapping of gene-sets, modules, and the incorporation of other non-protein-coding entities such as microRNAs.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA.
| | - Jan Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA
| | - Michaela Oswald
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA
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22
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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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23
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Abstract
OBJECTIVE Microarray-related studies often involve a very large number of genes and small sample size. Cross-validating or bootstrapping is therefore imperative to obtain a fair assessment of the prediction/classification performance of a gene signature. A deficiency of these methods is the reduced training sample size because of the partition process in cross-validation and sampling with replacement in bootstrapping. To address this problem, we aim to obtain a prediction performance estimate that strikes a good balance between bias and variance and has a small root mean squared error. METHODS We propose to make a one-step extrapolation from the fitted learning curve to estimate the prediction/classification performance of the model trained by all the samples. RESULTS Simulation studies show that the method strikes a good balance between bias and variance and has a small root mean squared error. Three microarray data sets are used for demonstration. CONCLUSIONS Our method is advocated to estimate the prediction performance of a gene signature derived from a small study.
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Affiliation(s)
- Ling-Yi Wang
- Research Center for Genes, Environment and Human Health, and Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Department of Medical Research, Tzu Chi General Hospital, Hualien, Taiwan
| | - Wen-Chung Lee
- Research Center for Genes, Environment and Human Health, and Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
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24
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Zang G, Gustafsson K, Jamalpour M, Hong J, Genové G, Welsh M. Vascular dysfunction and increased metastasis of B16F10 melanomas in Shb deficient mice as compared with their wild type counterparts. BMC Cancer 2015; 15:234. [PMID: 25885274 PMCID: PMC4392795 DOI: 10.1186/s12885-015-1269-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/25/2015] [Indexed: 02/03/2023] Open
Abstract
Background Shb is a signaling protein downstream of vascular endothelial growth factor receptor-2 and Shb deficiency has been found to restrict tumor angiogenesis. The present study was performed in order to assess metastasis in Shb deficiency using B16F10 melanoma cells. Methods B16F10 melanoma cells were inoculated subcutaneously on wild type or Shb +/− mice. Primary tumors were resected and lung metastasis determined after tumor relapse. Lung metastasis was also assessed after bone marrow transplantation of wild type bone marrow to Shb +/− recipients and Shb +/− bone marrow to wild type recipients. Primary tumors were subject to immunofluorescence staining for CD31, VE-cadherin, desmin and CD8, RNA isolation and isolation of vascular fragments for further RNA isolation. RNA was used for real-time RT-PCR and microarray analysis. Results Numbers of lung metastases were increased in Shb +/− or −/− mice and this coincided with reduced pericyte coverage and increased vascular permeability. Gene expression profiling of vascular fragments isolated from primary tumors and total tumor RNA revealed decreased expression of different markers for cytotoxic T cells in tumors grown on Shb +/− mice, suggesting that vascular aberrations caused altered immune responses. Conclusions It is concluded that a unique combinatorial response of increased vascular permeability and reduced recruitment of cytotoxic CD8+ cells occurs as a consequence of Shb deficiency in B16F10 melanomas. These changes may promote tumor cell intravasation and metastasis. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1269-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangxiang Zang
- Department of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden. .,Present address: Department of Medical Bioscience, Umeå University, Umeå, Sweden.
| | - Karin Gustafsson
- Department of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden.
| | - Maria Jamalpour
- Department of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden.
| | - JongWook Hong
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Guillem Genové
- Department of Medical Biochemistry and Biophysics, Division of Vascular Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Michael Welsh
- Department of Medical Cell Biology, Uppsala University, Box 571, Husargatan 3, 75123, Uppsala, Sweden.
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26
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The role of BRAF mutation in patients with high-risk malignant melanoma treated with high-dose adjuvant interferon therapy. Med Oncol 2014; 32:440. [DOI: 10.1007/s12032-014-0440-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
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27
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van Kempen LC, Redpath M, Robert C, Spatz A. Molecular pathology of cutaneous melanoma. Melanoma Manag 2014; 1:151-164. [PMID: 30190820 DOI: 10.2217/mmt.14.23] [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: 12/20/2022] Open
Abstract
Cutaneous melanoma is associated with strong prognostic phenotypic features, such as gender, Breslow's thickness and ulceration, although the biological significance of these variables is largely unknown. It is likely that these features are surrogates of important biological events rather than directly promoting cutaneous melanoma progression. In this article, we address the molecular mechanisms that drive these phenotypic changes. Furthermore, we present a comprehensive overview of recurrent genetic abnormalities, both germline and somatic, in relation to cutaneous melanoma subtypes, ultraviolet exposure and anatomical localization, as well as pre-existing and targeted therapy-induced mutations that may contribute to resistance. The increasing knowledge of critically important oncogenes and tumor-suppressor genes is promoting a transition in melanoma diagnosis, in which single-gene testing will be replaced by multiplex and multidimensional analyses that combine classical histopathological characteristics with the molecular profile for the prognostication and selection of melanoma therapy.
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Affiliation(s)
- Léon C van Kempen
- McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada.,McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada
| | - Margaret Redpath
- McGill University, Montreal, QC, Canada.,McGill University, Montreal, QC, Canada
| | - Caroline Robert
- Gustave Roussy Cancer Institute, Villejuif, Paris, France.,Gustave Roussy Cancer Institute, Villejuif, Paris, France
| | - Alan Spatz
- McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Department of Pathology, Jewish General Hospital, 3755 Cote Ste Catherine, Montreal, QC, H3T 1E2, Canada.,McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Department of Pathology, Jewish General Hospital, 3755 Cote Ste Catherine, Montreal, QC, H3T 1E2, Canada
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Hersey P, Kakavand H, Wilmott J, van der Westhuizen A, Gallagher S, Gowrishankar K, Scolyer R. How anti-PD1 treatments are changing the management of melanoma. Melanoma Manag 2014; 1:165-172. [PMID: 30190821 PMCID: PMC6094707 DOI: 10.2217/mmt.14.14] [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: 12/18/2022] Open
Abstract
The introduction of immunotherapy based on the blockade of the PD1/PD-L1 checkpoints has been associated with high response rates and durable remissions of disease in patients with metastatic melanoma, to the extent that it is now considered the standard of care for a wide range of patients, irrespective of their BRAF or NRAS mutation status. In addition, more frequent follow-up of patients who are at high risk of recurrence after surgical treatment appears to be justified, as does neoadjuvant treatments in order to render patients treatable by surgery. The limitations of this treatment include failure of some patients to respond, a low rate of complete responses and relapses of the disease during treatment. New initiatives in order to overcome these limitations include the identification of biomarkers for the selection responders and evaluations of treatment combinations that will increase responses and their durability. The latter includes combinations with antibodies against other checkpoints on T cells and cotreatments with inhibitors of resistance pathways in melanoma.
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Affiliation(s)
- Peter Hersey
- Kolling Institute, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
- Melanoma Institute of Australia, Rocklands Road, North Sydney, NSW, Australia
| | - Hojabr Kakavand
- Melanoma Institute of Australia, Rocklands Road, North Sydney, NSW, Australia
- Department of Anatomical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - James Wilmott
- Melanoma Institute of Australia, Rocklands Road, North Sydney, NSW, Australia
- Department of Anatomical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Stuart Gallagher
- Kolling Institute, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | | | - Richard Scolyer
- Melanoma Institute of Australia, Rocklands Road, North Sydney, NSW, Australia
- Department of Anatomical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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29
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Downregulation of reversion-inducing cysteine-rich protein with Kazal motifs in malignant melanoma: inverse correlation with membrane-type 1-matrix metalloproteinase and tissue inhibitor of metalloproteinase 2. Melanoma Res 2014; 24:32-9. [PMID: 24335752 DOI: 10.1097/cmr.0000000000000039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The invasive phenotype of many tumors is associated with an imbalance between the matrix metalloproteinases (MMPs) and their inhibitors, tissue inhibitors of metalloproteinases (TIMPs), and the membrane-anchored reversion-inducing cysteine-rich protein with Kazal motifs (RECK). RECK inhibits MMP-2, MMP-9, and MT1-MMP, and has been linked to patient survival and better prognosis in several types of tumors. However, despite the wide implication of these MMPs in melanoma establishment and progression, the role of RECK in this type of tumor is still unknown. Here, we analyzed the expression of RECK, TIMP1, TIMP2, TIMP3, MT1MMP, MMP2, and MMP9 in two publicly available melanoma microarray datasets and in a panel of human melanoma cell lines. We found that RECK is downregulated in malignant melanoma, accompanied by upregulation of MT1MMP and TIMP2. In both datasets, we observed that the group of samples displaying higher RECK levels show lower median expression levels of MT1MMP and TIMP2 and higher levels of TIMP3. When tested in a sample-wise manner, these correlations were statistically significant. Inverse correlations between RECK, MT1MMP, and TIMP2 were verified in a panel of human melanoma cell lines and in a further reduced model that includes a pair of matched primary tumor-derived and metastasis-derived cell lines. Taken together, our data indicate a consistent correlation between RECK, MT1MMP, and TIMP2 across different models of clinical samples and cell lines and suggest evidence of the potential use of this subset of genes as a gene signature for diagnosing melanoma.
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30
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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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Tringali C, Silvestri I, Testa F, Baldassari P, Anastasia L, Mortarini R, Anichini A, López-Requena A, Tettamanti G, Venerando B. Molecular subtyping of metastatic melanoma based on cell ganglioside metabolism profiles. BMC Cancer 2014; 14:560. [PMID: 25085576 PMCID: PMC4132924 DOI: 10.1186/1471-2407-14-560] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In addition to alterations concerning the expression of oncogenes and onco-suppressors, melanoma is characterized by the presence of distinctive gangliosides (sialic acid carrying glycosphingolipids). Gangliosides strongly control cell surface dynamics and signaling; therefore, it could be assumed that these alterations are linked to modifications of cell behavior acquired by the tumor. On these bases, this work investigated the correlations between melanoma cell ganglioside metabolism profiles and the biological features of the tumor and the survival of patients. METHODS Melanoma cell lines were established from surgical specimens of AJCC stage III and IV melanoma patients. Sphingolipid analysis was carried out on melanoma cell lines and melanocytes through cell metabolic labeling employing [3-3H]sphingosine and by FACS. N-glycolyl GM3 was identified employing the 14 F7 antibody. Gene expression was assayed by Real Time PCR. Cell invasiveness was assayed through a Matrigel invasion assay; cell proliferation was determined through the soft agar assay, MTT, and [3H] thymidine incorporation. Statistical analysis was performed using XLSTAT software for melanoma hierarchical clustering based on ganglioside profile, the Kaplan-Meier method, the log-rank (Mantel-Cox) test, and the Mantel-Haenszel test for survival analysis. RESULTS Based on the ganglioside profiles, through a hierarchical clustering, we classified melanoma cells isolated from patients into three clusters: 1) cluster 1, characterized by high content of GM3, mainly in the form of N-glycolyl GM3, and GD3; 2) cluster 2, characterized by the appearance of complex gangliosides and by a low content of GM3; 3) cluster 3, which showed an intermediate phenotype between cluster 1 and cluster 3. Moreover, our data demonstrated that: a) a correlation could be traced between patients' survival and clusters based on ganglioside profiles, with cluster 1 showing the worst survival; b) the expression of several enzymes (sialidase NEU3, GM2 and GM1 synthases) involved in ganglioside metabolism was associated with patients' survival; c) melanoma clusters showed different malignant features such as growth in soft agar, invasiveness, expression of anti-apoptotic proteins. CONCLUSIONS Ganglioside profile and metabolism is strictly interconnected with melanoma aggressiveness. Therefore, the profiling of melanoma gangliosides and enzymes involved in their metabolism could represent a useful prognostic and diagnostic tool.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Bruno Venerando
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Milan, Italy.
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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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Alvino E, Passarelli F, Cannavò E, Fortes C, Mastroeni S, Caporali S, Jiricny J, Cappellini GCA, Scoppola A, Marchetti P, Modesti A, D’Atri S. High expression of the mismatch repair protein MSH6 is associated with poor patient survival in melanoma. Am J Clin Pathol 2014; 142:121-32. [PMID: 24926095 DOI: 10.1309/ajcpcx2d9yulbblg] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES The outcome of patients with primary melanoma (PM) cannot be completely explained based on currently adopted clinical-histopathologic criteria. In this study, we evaluated the potential prognostic value of mismatch repair protein expression in PMs. METHODS We examined the immunohistochemical staining of mismatch repair proteins in 18 benign nevi and 101 stage I to III PMs and investigated their association with tumor clinicopathologic variables and melanoma mortality. RESULTS Expression of MSH2, MLH1, and PMS2 was high in benign nevi and reduced in a subset of PMs. Conversely, MSH6 expression was absent or extremely low in benign nevi and increased in a subset of PMs. In the multivariate analysis, including sex, age, Breslow thickness, and ulceration, high MSH6 expression in PMs (ie, immunostaining in >20% of tumor cells) was significantly associated with an increased risk of melanoma mortality (relative risk, 3.76; 95% confidence interval, 1.12-12.70). CONCLUSIONS MSH6 protein expression can be a valuable marker to improve prognosis assessment in PMs.
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Affiliation(s)
- Ester Alvino
- Institute of Translational Pharmacology, National Council of Research, Rome, Italy
| | | | - Elda Cannavò
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Cristina Fortes
- Epidemiology Unit, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
| | - Simona Mastroeni
- Epidemiology Unit, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
| | - Simona Caporali
- Laboratory of Molecular Oncology, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | | | - Alessandro Scoppola
- Department of Oncology and Dermatological Oncology, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
| | - Paolo Marchetti
- Department of Oncology, Sant’Andrea Hospital, University of Rome “La Sapienza,” Rome, Italy
| | - Andrea Modesti
- Department of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata,” Rome, Italy
| | - Stefania D’Atri
- Laboratory of Molecular Oncology, Istituto Dermopatico dell’Immacolata-IRCCS, Rome, Italy
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Blumenberg M. Skinomics: past, present and future for diagnostic microarray studies in dermatology. Expert Rev Mol Diagn 2014; 13:885-94. [PMID: 24151852 DOI: 10.1586/14737159.2013.846827] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Easily accessible, skin was among the first targets analyzed using 'omics' and dermatology embraced the approaches very early. Microarrays have been used to define disease markers, identify transcriptional changes and even trace the course of treatment. Melanoma and psoriasis have been explored using microarrays. Particularly noteworthy is the multinational mapping of psoriasis susceptibility loci. The transcriptional changes in psoriasis have been identified using hundreds of biopsies. Epidermal keratinocytes have been studied because they respond to UV light, infections, inflammatory and immunomodulating cytokines, toxins and so on. Epidermal differentiation genes are being characterized and are expressed in human epidermal stem cells. Exciting discoveries defining human skin microbiomes have opened a new field of research with great medical potential. Specific to dermatology, the non-invasive skin sampling for microarray studies, using tape stripping, has been developed; it promises to advance dermatology toward 'omics' techniques directly applicable to the personalized medicine of the future.
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Affiliation(s)
- Miroslav Blumenberg
- The R.O. Perelman Department of Dermatology, Department of Biochemistry and Molecular Pharmacology, the NYU Cancer Institute, NYU Langone Medical Center, NYU School of Medicine, 455 First Avenue, P.H.B. Room 874, New York NY 10016, USA
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35
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Camisaschi C, Vallacchi V, Castelli C, Rivoltini L, Rodolfo M. Immune cells in the melanoma microenvironment hold information for prediction of the risk of recurrence and response to treatment. Expert Rev Mol Diagn 2014; 14:643-6. [PMID: 24914691 DOI: 10.1586/14737159.2014.928206] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Melanoma is an immunogenic tumor and immunotherapy treatment has established an increase in disease-free and overall survival in melanoma patients. However, a complex network of immunosuppressive mechanisms has been demonstrated to occur at the tumor site and in locoregional immune districts, such as sentinel lymph nodes (SLNs). The interplay between tumor cells and the local microenvironment leads to a tumor-driven shaping of the immune response that results in a heterogeneous cellular and molecular composition of tumor infiltrating lymphocytes (TILs). Several studies have reported the potential prognostic value of TILs infiltrating primary tumors and the association of 'immune signature' in SLNs and in melanoma metastases with prognosis and responsiveness to immunotherapeutic approaches. However, a systematic and deeper characterization of the local immunological status of TILs and SLNs is still required to refine melanoma stage classification.
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Affiliation(s)
- Chiara Camisaschi
- Unit of Immunotherapy, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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36
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Andrews MC, Woods K, Cebon J, Behren A. Evolving role of tumor antigens for future melanoma therapies. Future Oncol 2014; 10:1457-68. [DOI: 10.2217/fon.14.84] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT: Human tumor rejection antigens recognized by T lymphocytes were first defined in the early 1990s and the identification of shared tumor-restricted antigens sparked hopes for the development of a therapeutic vaccination to treat cancer, including melanoma. Despite decades of intense preclinical and clinical research, the success of anticancer vaccines based on these antigens has been limited. While melanoma is a highly immunogenic tumor, the ability to prime immunity with vaccines has not generally translated into objective disease regression. However, with the development of small molecules targeting oncogenic proteins, such as V600-mutated BRAF, and immune checkpoint inhibitors with demonstrable long-lasting clinical benefit, new opportunities for antigen-targeted directed therapies are emerging.
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Affiliation(s)
- Miles C Andrews
- Ludwig Institute for Cancer Research Ltd, Olivia Newton-John Cancer & Wellness Centre, Cancer Immunobiology, Heidelberg, VIC, Australia
- Medical Oncology, Joint Ludwig–Austin Oncology Unit, Austin Health, Victoria, Australia
| | - Katherine Woods
- Ludwig Institute for Cancer Research Ltd, Olivia Newton-John Cancer & Wellness Centre, Cancer Immunobiology, Heidelberg, VIC, Australia
| | - Jonathan Cebon
- Ludwig Institute for Cancer Research Ltd, Olivia Newton-John Cancer & Wellness Centre, Cancer Immunobiology, Heidelberg, VIC, Australia
- Medical Oncology, Joint Ludwig–Austin Oncology Unit, Austin Health, Victoria, Australia
| | - Andreas Behren
- Ludwig Institute for Cancer Research Ltd, Olivia Newton-John Cancer & Wellness Centre, Cancer Immunobiology, Heidelberg, VIC, Australia
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Luo X, Mitra D, Sullivan RJ, Wittner BS, Kimura AM, Pan S, Hoang MP, Brannigan BW, Lawrence DP, Flaherty KT, Sequist LV, McMahon M, Bosenberg MW, Stott SL, Ting DT, Ramaswamy S, Toner M, Fisher DE, Maheswaran S, Haber DA. Isolation and molecular characterization of circulating melanoma cells. Cell Rep 2014; 7:645-53. [PMID: 24746818 PMCID: PMC4079008 DOI: 10.1016/j.celrep.2014.03.039] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/18/2014] [Accepted: 03/12/2014] [Indexed: 02/04/2023] Open
Abstract
Melanoma is an invasive malignancy with a high frequency of blood-borne metastases, but circulating tumor cells (CTCs) have not been readily isolated. We adapted microfluidic CTC capture to a tamoxifen-driven B-RAF/PTEN mouse melanoma model. CTCs were detected in all tumor-bearing mice and rapidly declined after B-RAF inhibitor treatment. CTCs were shed early from localized tumors, and a short course of B-RAF inhibition following surgical resection was sufficient to dramatically suppress distant metastases. The large number of CTCs in melanoma-bearing mice enabled a comparison of RNA-sequencing profiles with matched primary tumors. A mouse melanoma CTC-derived signature correlated with invasiveness and cellular motility in human melanoma. CTCs were detected in smaller numbers in patients with metastatic melanoma and declined with successful B-RAF-targeted therapy. Together, the capture and molecular characterization of CTCs provide insight into the hematogenous spread of melanoma.
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Affiliation(s)
- Xi Luo
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Devarati Mitra
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Anya M Kimura
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Shiwei Pan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Brian W Brannigan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Donald P Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Martin McMahon
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marcus W Bosenberg
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shannon L Stott
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Engineering in Medicine, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Mehmet Toner
- Center for Engineering in Medicine, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David E Fisher
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA.
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Griewank KG, Scolyer RA, Thompson JF, Flaherty KT, Schadendorf D, Murali R. Genetic alterations and personalized medicine in melanoma: progress and future prospects. J Natl Cancer Inst 2014; 106:djt435. [PMID: 24511108 DOI: 10.1093/jnci/djt435] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
High-throughput sequencing technologies are providing new insights into the genetic alterations involved in melanomagenesis. It appears likely that most genetic events important in the pathogenesis of melanoma will be discovered over the next few years. Genetic analysis is also increasingly being used to direct patient care. In parallel with the discovery of new genes and the elucidation of molecular pathways important in the development of melanoma, therapies targeting these pathways are becoming available. In other words, the age of personalized medicine has arrived, characterized by molecular profiling of melanoma to identify the relevant genetic alterations and the abnormal signaling mechanisms involved, followed by selection of optimal, individualized therapies. In this review, we summarize the key genetic alterations in melanoma and the development of targeted agents against melanomas bearing specific mutations. These developments in melanoma serve as a model for the implementation of personalized medicine for patients with all cancers.
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Affiliation(s)
- Klaus G Griewank
- Affiliations of authors: Department of Dermatology, University Hospital, University Duisburg-Essen, Essen, Germany (KGG, DS); Royal Prince Alfred Hospital, Camperdown, NSW, Australia (RAS); University of Sydney, Camperdown, NSW, Australia (RAS, JFT); Melanoma Institute Australia, North Sydney, NSW, Australia (RAS, JFT); Center for Melanoma, Massachusetts General Hospital Cancer Center, Boston, MA (KTF); Department of Pathology, and Center for Molecular Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY (RM)
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Schramm SJ, Li SS, Jayaswal V, Fung DCY, Campain AE, Pang CNI, Scolyer RA, Yang YH, Mann GJ, Wilkins MR. Disturbed protein-protein interaction networks in metastatic melanoma are associated with worse prognosis and increased functional mutation burden. Pigment Cell Melanoma Res 2013; 26:708-22. [PMID: 23738911 DOI: 10.1111/pcmr.12126] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/30/2013] [Indexed: 12/15/2022]
Abstract
For disseminated melanoma, new prognostic biomarkers and therapeutic targets are urgently needed. The organization of protein-protein interaction networks was assessed via the transcriptomes of four independent studies of metastatic melanoma and related to clinical outcome and MAP-kinase pathway mutations (BRAF/NRAS). We also examined patient outcome-related differences in a predicted network of microRNAs and their targets. The 32 hub genes with the most reproducible survival-related disturbances in co-expression with their protein partner genes included oncogenes and tumor suppressors, previously known correlates of prognosis, and other proteins not previously associated with melanoma outcome. Notably, this network-based gene set could classify patients according to clinical outcomes with 67-80% accuracy among cohorts. Reproducibly disturbed networks were also more likely to have a higher functional mutation burden than would be expected by chance. The disturbed regions of networks are therefore markers of clinically relevant, selectable tumor evolution in melanoma which may carry driver mutations.
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Affiliation(s)
- Sarah-Jane Schramm
- Sydney Medical School, The University of Sydney at Westmead Millennium Institute for Medical Research, Sydney, NSW, Australia
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Transcriptome profiling identifies HMGA2 as a biomarker of melanoma progression and prognosis. J Invest Dermatol 2013; 133:2585-2592. [PMID: 23633021 DOI: 10.1038/jid.2013.197] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 12/16/2022]
Abstract
The genetic alterations contributing to melanoma pathogenesis are incompletely defined, and few independent prognostic features have been identified beyond the clinicopathological characteristics of the primary tumor. We used transcriptome profiling of 46 primary melanomas, 12 melanoma metastases, and 16 normal skin (N) samples to find genes associated with melanoma development and progression. Results were confirmed using immunohistochemistry and real-time PCR and replicated in an independent set of 330 melanomas using AQUA analysis of tissue microarray (TMA). Transcriptome profiling revealed that transcription factor HMGA2, previously unrecognized in melanoma pathogenesis, is significantly upregulated in primary melanoma and metastases (P-values=1.2 × 10(-7) and 9 × 10(-5)) compared with N. HMGA2 overexpression is associated with BRAF/NRAS mutations (P=0.0002). Cox proportional hazard regression model and log-rank test showed that HMGA2 is independently associated with disease-free survival (hazard ratio (HR)=6.3, 95% confidence interval (CI)=1.8-22.3, P=0.004), overall survival (OS) (stratified log-rank P=0.008), and distant metastases-free survival (HR=6.4, 95% CI=1.4-29.7, P=0.018) after adjusting for American Joint Committee on Cancer (AJCC) stage and age at diagnosis. Survival analysis in an independent replication TMA of 330 melanomas confirmed the association of HMGA2 expression with OS (P=0.0211). Our study implicates HMGA2 in melanoma progression and demonstrates that HMGA2 overexpression can serve as an independent predictor of survival in melanoma.
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Liu W, Peng Y, Tobin DJ. A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis. PeerJ 2013; 1:e49. [PMID: 23638386 PMCID: PMC3628745 DOI: 10.7717/peerj.49] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/20/2013] [Indexed: 12/16/2022] Open
Abstract
Genome-wide microarray technology has facilitated the systematic discovery of diagnostic biomarkers of cancers and other pathologies. However, meta-analyses of published arrays often uncover significant inconsistencies that hinder advances in clinical practice. Here we present an integrated microarray analysis framework, based on a genome-wide relative significance (GWRS) and genome-wide global significance (GWGS) model. When applied to five microarray datasets on melanoma published between 2000 and 2011, this method revealed a new signature of 200 genes. When these were linked to so-called ‘melanoma driver’ genes involved in MAPK, Ca2+, and WNT signaling pathways we were able to produce a new 12-gene diagnostic biomarker signature for melanoma (i.e., EGFR, FGFR2, FGFR3, IL8, PTPRF, TNC, CXCL13, COL11A1, CHP2, SHC4, PPP2R2C, and WNT4). We have begun to experimentally validate a subset of these genes involved in MAPK signaling at the protein level, including CXCL13, COL11A1, PTPRF and SHC4 and found these to be over-expressed in metastatic and primary melanoma cells in vitro and in situ compared to melanocytes cultured from healthy skin epidermis and normal healthy human skin. While SHC4 has been reported previously to be associated to melanoma, this is the first time CXCL13, COL11A1, and PTPRF have been associated with melanoma on experimental validation. Our computational evaluation indicates that this 12-gene biomarker signature achieves excellent diagnostic power in distinguishing metastatic melanoma from normal skin and benign nevus. Further experimental validation of the role of these 12 genes in a new signaling network may provide new insights into the underlying biological mechanisms driving the progression of melanoma.
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Affiliation(s)
- Wanting Liu
- Department of Computing, University of Bradford , Great Britain ; Centre of Skin Sciences, University of Bradford , Great Britain
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4-Bromo-2-(piperidin-1-yl)thiazol-5-yl-phenyl methanone (12b) inhibits Na+/K(+)-ATPase and Ras oncogene activity in cancer cells. Eur J Med Chem 2013; 63:213-23. [PMID: 23474907 DOI: 10.1016/j.ejmech.2013.01.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 01/16/2013] [Accepted: 01/22/2013] [Indexed: 11/23/2022]
Abstract
The in vitro growth inhibitory activity of 26 thiazoles (including 4-halogeno-2,5-disubtituted-1,3-thiazoles) and 5 thienothiazoles was assessed on a panel of 6 human cancer cell lines, including glioma cell lines. (4-Chloro-2-(piperidin-1-yl)thiazol-5-yl)(phenyl)methanone (12a) and (4-bromo-2-(piperidin-1-yl)thiazol-5-yl)(phenyl)methanone (12b) displayed ~10 times greater in vitro growth inhibitory activity than perillyl alcohol (POH), which therapeutically benefits glioma patients through the inhibition of both alpha-1 Na(+)/K(+)-ATPase (NAK) and Ras oncogene activity. The in vitro cytostatic activities (as revealed by quantitative videomicroscopy) displayed by 12a and 12b were independent of the intrinsic resistance to pro-apoptotic stimuli associated with cancer cells. Compounds 12a and 12b displayed relatively similar inhibitory activities on purified guinea pig brain preparations that mainly express NAK alpha-2 and alpha-3 subunits, whereas only compound 12b was efficacious against purified guinea pig kidney preparations that mainly express the NAK alpha-1 subunit, which is also expressed in gliomas, melanomas and non-small-cell lung cancers NSCLCs.
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An attempt at a molecular prediction of metastasis in patients with primary cutaneous melanoma. PLoS One 2012; 7:e49865. [PMID: 23166783 PMCID: PMC3498185 DOI: 10.1371/journal.pone.0049865] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 10/15/2012] [Indexed: 12/31/2022] Open
Abstract
Background Current prognostic clinical and morphological parameters are insufficient to accurately predict metastasis in individual melanoma patients. Several studies have described gene expression signatures to predict survival or metastasis of primary melanoma patients, however the reproducibility among these studies is disappointingly low. Methodology/Principal Findings We followed extended REMARK/Gould Rothberg criteria to identify gene sets predictive for metastasis in patients with primary cutaneous melanoma. For class comparison, gene expression data from 116 patients with clinical stage I/II (no metastasis) and 72 with III/IV primary melanoma (with metastasis) at time of first diagnosis were used. Significance analysis of microarrays identified the top 50 differentially expressed genes. In an independent data set from a second cohort of 28 primary melanoma patients, these genes were analyzed by multivariate Cox regression analysis and leave-one-out cross validation for association with development of metastatic disease. In a multivariate Cox regression analysis, expression of the genes Ena/vasodilator-stimulated phosphoprotein-like (EVL) and CD24 antigen gave the best predictive value (p = 0.001; p = 0.017, respectively). A multivariate Cox proportional hazards model revealed these genes as a potential independent predictor, which may possibly add (both p = 0.01) to the predictive value of the most important morphological indicator, Breslow depth. Conclusion/Significance Combination of molecular with morphological information may potentially enable an improved prediction of metastasis in primary melanoma patients. A strength of the gene expression set is the small number of genes, which should allow easy reevaluation in independent data sets and adequately designed clinical trials.
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BRAF mutation, NRAS mutation, and the absence of an immune-related expressed gene profile predict poor outcome in patients with stage III melanoma. J Invest Dermatol 2012; 133:509-17. [PMID: 22931913 DOI: 10.1038/jid.2012.283] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Prediction of outcome for melanoma patients with surgically resected macroscopic nodal metastases is very imprecise. We performed a comprehensive clinico-pathologic assessment of fresh-frozen macroscopic nodal metastases and the preceding primary melanoma, somatic mutation profiling, and gene expression profiling to identify determinants of outcome in 79 melanoma patients. In addition to disease stage <II at initial presentation, the following clinical and pathologic factors were independent predictors of improved outcome (odds ratios for survival >4 years, 90% confidence interval): the presence of a nodular component in the primary melanoma (6.8, 0.6-76.0), and small cell size (11.1, 0.8-100.0) or low pigmentation (3.0, 0.8-100.0) in the nodal metastases. Absence of BRAF mutation (20.0, 1.0-1000.0) or NRAS mutation (16.7, 0.6-1000.0) were both favorable prognostic factors. A 46-gene expression signature with strong overrepresentation of immune response genes was predictive of better survival (10.9, 0.4-325.6); in the full cohort, median survival was >100 months in those with the signature, but 10 months in those without. This relationship was validated in two previously published independent stage III melanoma data sets. We conclude that the presence of BRAF mutation, NRAS mutation, and the absence of an immune-related expressed gene profile predict poor outcome in melanoma patients with macroscopic stage III disease.
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