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Clarke EL, Wade RG, Magee D, Newton-Bishop J, Treanor D. Image analysis of cutaneous melanoma histology: a systematic review and meta-analysis. Sci Rep 2023; 13:4774. [PMID: 36959221 PMCID: PMC10036523 DOI: 10.1038/s41598-023-31526-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/14/2023] [Indexed: 03/25/2023] Open
Abstract
The current subjective histopathological assessment of cutaneous melanoma is challenging. The application of image analysis algorithms to histological images may facilitate improvements in workflow and prognostication. To date, several individual algorithms applied to melanoma histological images have been reported with variations in approach and reported accuracies. Histological digital images can be created using a camera mounted on a light microscope, or through whole slide image (WSI) generation using a whole slide scanner. Before any such tool could be integrated into clinical workflow, the accuracy of the technology should be carefully evaluated and summarised. Therefore, the objective of this review was to evaluate the accuracy of existing image analysis algorithms applied to digital histological images of cutaneous melanoma. Database searching of PubMed and Embase from inception to 11th March 2022 was conducted alongside citation checking and examining reports from organisations. All studies reporting accuracy of any image analysis applied to histological images of cutaneous melanoma, were included. The reference standard was any histological assessment of haematoxylin and eosin-stained slides and/or immunohistochemical staining. Citations were independently deduplicated and screened by two review authors and disagreements were resolved through discussion. The data was extracted concerning study demographics; type of image analysis; type of reference standard; conditions included and test statistics to construct 2 × 2 tables. Data was extracted in accordance with our protocol and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses-Diagnostic Test Accuracy (PRISMA-DTA) Statement. A bivariate random-effects meta-analysis was used to estimate summary sensitivities and specificities with 95% confidence intervals (CI). Assessment of methodological quality was conducted using a tailored version of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. The primary outcome was the pooled sensitivity and specificity of image analysis applied to cutaneous melanoma histological images. Sixteen studies were included in the systematic review, representing 4,888 specimens. Six studies were included in the meta-analysis. The mean sensitivity and specificity of automated image analysis algorithms applied to melanoma histological images was 90% (CI 82%, 95%) and 92% (CI 79%, 97%), respectively. Based on limited and heterogeneous data, image analysis appears to offer high accuracy when applied to histological images of cutaneous melanoma. However, given the early exploratory nature of these studies, further development work is necessary to improve their performance.
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Affiliation(s)
- Emily L Clarke
- Department of Histopathology, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
- Division of Pathology and Data Analytics, Leeds Institute of Cancer and Pathology, University of Leeds, Beckett Street, Leeds, LS9 7TF, UK.
| | - Ryckie G Wade
- Leeds Institute for Medical Research, University of Leeds, Leeds, UK
| | - Derek Magee
- School of Computing, University of Leeds, Leeds, UK
| | - Julia Newton-Bishop
- Division of Pathology and Data Analytics, Leeds Institute of Cancer and Pathology, University of Leeds, Beckett Street, Leeds, LS9 7TF, UK
| | - Darren Treanor
- Department of Histopathology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Division of Pathology and Data Analytics, Leeds Institute of Cancer and Pathology, University of Leeds, Beckett Street, Leeds, LS9 7TF, UK
- Department of Clinical Pathology, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
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2
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Kim JY, Cho H, Yoo J, Kim GW, Jeon YH, Lee SW, Kwon SH. HDAC8 Deacetylates HIF-1α and Enhances Its Protein Stability to Promote Tumor Growth and Migration in Melanoma. Cancers (Basel) 2023; 15:cancers15041123. [PMID: 36831463 PMCID: PMC9953989 DOI: 10.3390/cancers15041123] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Melanoma is the most lethal type of skin cancer, and it causes more than 55,000 deaths annually. Although regional melanoma can be surgically removed, once melanoma metastasizes to other regions of the body, the survival rate drops dramatically. The current treatment options are chemotherapy, immunotherapy, and targeted therapy. However, the low response rate and the development of resistance necessitate the search for a novel therapeutic target in melanoma. Hypoxia-inducible factor-1 α (HIF-1α) is overexpressed in melanoma and plays a crucial role in driving malignant transformation in cancer cells. Here, we identified that histone deacetylase 8 (HDAC8) enhances the protein stability of HIF-1α. HDAC8 directly binds to and deacetylates HIF-1α, thereby promoting its protein stability. This, in turn, upregulates the transcriptional activity of HIF-1α and promotes the expressions of its target genes, such as hexokinase 2 (HK2) and glucose transporter 1 (GLUT1). The inhibition of HDAC8 suppresses the proliferation and metastasis of melanoma cells. Furthermore, HDAC8 is correlated with HIF1A expression and poor prognosis in samples from patients with melanoma. These findings uncover a novel epigenetic mechanism that maintains HIF-1α stability and implicates the potential of HDAC8 inhibitors for melanoma therapy.
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3
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Conway K, Tsai YS, Edmiston SN, Parker JS, Parrish EA, Hao H, Kuan PF, Scott GA, Frank JS, Googe P, Ollila DW, Thomas NE. Characterization of the CpG Island Hypermethylated Phenotype Subclass in Primary Melanomas. J Invest Dermatol 2022; 142:1869-1881.e10. [PMID: 34843679 PMCID: PMC9135958 DOI: 10.1016/j.jid.2021.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022]
Abstract
Cutaneous melanoma can be lethal even if detected at an early stage. Epigenetic profiling may facilitate the identification of aggressive primary melanomas with unfavorable outcomes. We performed clustering of whole-genome methylation data to identify subclasses that were then assessed for survival, clinical features, methylation patterns, and biological pathways. Among 89 cutaneous primary invasive melanomas, we identified three methylation subclasses exhibiting low methylation, intermediate methylation, or hypermethylation of CpG islands, known as the CpG island methylator phenotype (CIMP). CIMP melanomas occurred as early as tumor stage 1b and, compared with low-methylation melanomas, were associated with age at diagnosis ≥65 years, lentigo maligna melanoma histologic subtype, presence of ulceration, higher American Joint Committee on Cancer stage and tumor stage, and lower tumor-infiltrating lymphocyte grade (all P < 0.05). Patients with CIMP melanomas had worse melanoma-specific survival (hazard ratio = 11.84; confidence interval = 4.65‒30.20) than those with low-methylation melanomas, adjusted for age, sex, American Joint Committee on Cancer stage, and tumor-infiltrating lymphocyte grade. Genes hypermethylated in CIMP compared with those in low-methylation melanomas included PTEN, VDR, PD-L1, TET2, and gene sets related to development/differentiation, the extracellular matrix, and immunity. CIMP melanomas exhibited hypermethylation of genes important in melanoma progression and tumor immunity, and although present in some early melanomas, CIMP was associated with worse survival independent of known prognostic factors.
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Affiliation(s)
- Kathleen Conway
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Yihsuan S Tsai
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon N Edmiston
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eloise A Parrish
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Honglin Hao
- Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pei Fen Kuan
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Glynis A Scott
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA; Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jill S Frank
- Department of Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Paul Googe
- Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pathology and Lab Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David W Ollila
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancy E Thomas
- Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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4
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Bakr MN, Takahashi H, Kikuchi Y. Analysis of Melanoma Gene Expression Signatures at the Single-Cell Level Uncovers 45-Gene Signature Related to Prognosis. Biomedicines 2022; 10:biomedicines10071478. [PMID: 35884783 PMCID: PMC9313451 DOI: 10.3390/biomedicines10071478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/12/2022] [Accepted: 06/19/2022] [Indexed: 11/16/2022] Open
Abstract
Since the current melanoma clinicopathological staging system remains restricted to predicting survival outcomes, establishing precise prognostic targets is needed. Here, we used gene expression signature (GES) classification and Cox regression analyses to biologically characterize melanoma cells at the single-cell level and construct a prognosis-related gene signature for melanoma. By analyzing publicly available scRNA-seq data, we identified six distinct GESs (named: “Anti-apoptosis”, “Immune cell interactions”, “Melanogenesis”, “Ribosomal biogenesis”, “Extracellular structure organization”, and “Epithelial-Mesenchymal Transition (EMT)”). We verified these GESs in the bulk RNA-seq data of patients with skin cutaneous melanoma (SKCM) from The Cancer Genome Atlas (TCGA). Four GESs (“Immune cell interactions”, “Melanogenesis”, “Ribosomal biogenesis”, and “Extracellular structure organization”) were significantly correlated with prognosis (p = 1.08 × 10−5, p = 0.042, p = 0.001, and p = 0.031, respectively). We identified a prognostic signature of melanoma composed of 45 genes (MPS_45). MPS_45 was validated in TCGA-SKCM (HR = 1.82, p = 9.08 × 10−6) and three other melanoma datasets (GSE65904: HR = 1.73, p = 0.006; GSE19234: HR = 3.83, p = 0.002; and GSE53118: HR = 1.85, p = 0.037). MPS_45 was independently associated with survival (p = 0.002) and was proved to have a high potential for predicting prognosis in melanoma patients.
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Affiliation(s)
- Mohamed Nabil Bakr
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- National Institute of Oceanography and Fisheries (NIOF), Cairo 11516, Egypt
| | - Haruko Takahashi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Correspondence: (H.T.); (Y.K.); Tel.: +81-82-424-7440 (Y.K.)
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan;
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Correspondence: (H.T.); (Y.K.); Tel.: +81-82-424-7440 (Y.K.)
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5
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Kramer ET, Godoy PM, Kaufman CK. TRANSCRIPTIONAL PROFILE AND CHROMATIN ACCESSIBILITY IN ZEBRAFISH MELANOCYTES AND MELANOMA TUMORS. G3-GENES GENOMES GENETICS 2021; 12:6428538. [PMID: 34791221 PMCID: PMC8727958 DOI: 10.1093/g3journal/jkab379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/02/2021] [Indexed: 11/14/2022]
Abstract
Transcriptional and epigenetic characterization of melanocytes and melanoma cells isolated from their in vivo context promises to unveil key differences between these developmentally related normal and cancer cell populations. We therefore engineered an enhanced Danio rerio (zebrafish) melanoma model with fluorescently labeled melanocytes to allow for isolation of normal (wild type) and premalignant (BRAFV600E-mutant) populations for comparison to fully transformed BRAFV600E-mutant, p53 loss-of-function melanoma cells. Using fluorescence-activated cell sorting to isolate these populations, we performed high-quality RNA- and ATAC-seq on sorted zebrafish melanocytes vs. melanoma cells, which we provide as a resource here. Melanocytes had consistent transcriptional and accessibility profiles, as did melanoma cells. Comparing melanocytes and melanoma, we note 4128 differentially expressed genes and 56,936 differentially accessible regions with overall gene expression profiles analogous to human melanocytes and the pigmentation melanoma subtype. Combining the RNA- and ATAC-seq data surprisingly revealed that increased chromatin accessibility did not always correspond with increased gene expression, suggesting that though there is widespread dysregulation in chromatin accessibility in melanoma, there is a potentially more refined gene expression program driving cancerous melanoma. These data serve as a resource to identify candidate regulators of the normal vs. diseased states in a genetically controlled in vivo context.
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Affiliation(s)
- Eva T Kramer
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO 63110 USA
| | - Paula M Godoy
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO 63110 USA
| | - Charles K Kaufman
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO 63110 USA
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6
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Ismail H, Helby J, Hölmich LR, H Chakera A, Bastholt L, Klyver H, Sjøgren P, Schmidt H, Schöllhammer L, Nordestgaard BG, Bojesen SE. Genetic predisposition to long telomeres is associated with increased mortality after melanoma: A study of 2101 melanoma patients from hospital clinics and the general population. Pigment Cell Melanoma Res 2021; 34:946-954. [PMID: 33749133 DOI: 10.1111/pcmr.12971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/17/2021] [Accepted: 03/13/2021] [Indexed: 01/24/2023]
Abstract
Whether there is an association between measured and genetically predicted telomere length and melanoma mortality is unclear. We tested the hypothesis that measured and genetically predicted telomere length is associated with mortality after a melanoma diagnosis. We followed 2,101 patients with melanoma from hospital clinics and the general population for risk of death for up to 26 years. All had telomere length measured in DNA from leukocytes, and 2052 of these were genotyped for the three single nucleotide polymorphisms rs7726159 (TERT), rs1317082 (TERC), and rs2487999 (OBFC1); all three genotypes are associated with telomere length and combined into an allele count from 0 to 6. For each telomere-lengthening allele, the hazard ratios (HRs) for mortality in the age-adjusted and multivariable-adjusted Cox analysis were 1.12 (95% confidence interval: 1.02-1.23) and 1.11 (1.01-1.23). However, for each standard deviation increase in measured telomere length, HR for mortality was 0.97 (0.88-1.08). In conclusion, in more than 2000 melanoma patients from hospital clinics and from the general population, genetically predicted long telomeres were associated with increased mortality, but measured leukocyte telomere length was not.
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Affiliation(s)
- Hafsa Ismail
- Department of Clinical Biochemistry, The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, København, Denmark
| | - Jens Helby
- Department of Clinical Biochemistry, The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark.,Department of Hematology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Lisbet R Hölmich
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, København, Denmark.,Department of Plastic Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Annette H Chakera
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, København, Denmark.,Department of Plastic Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Lars Bastholt
- Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Helle Klyver
- Department of Plastic Surgery, Rigshospitalet, Copenhagen University Hospital, København, Denmark
| | - Pia Sjøgren
- Department of Plastic Surgery, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Schmidt
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Liv Schöllhammer
- Department of Plastic Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, København, Denmark.,Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital, Frederiksberg, Denmark
| | - Stig E Bojesen
- Department of Clinical Biochemistry, The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, København, Denmark.,Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital, Frederiksberg, Denmark
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7
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Netanely D, Leibou S, Parikh R, Stern N, Vaknine H, Brenner R, Amar S, Factor RH, Perluk T, Frand J, Nizri E, Hershkovitz D, Zemser-Werner V, Levy C, Shamir R. Classification of node-positive melanomas into prognostic subgroups using keratin, immune, and melanogenesis expression patterns. Oncogene 2021; 40:1792-1805. [PMID: 33564068 PMCID: PMC7946641 DOI: 10.1038/s41388-021-01665-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/08/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023]
Abstract
Cutaneous melanoma tumors are heterogeneous and show diverse responses to treatment. Identification of robust molecular biomarkers for classifying melanoma tumors into clinically distinct and homogenous subtypes is crucial for improving the diagnosis and treatment of the disease. In this study, we present a classification of melanoma tumors into four subtypes with different survival profiles based on three distinct gene expression signatures: keratin, immune, and melanogenesis. The melanogenesis expression pattern includes several genes that are characteristic of the melanosome organelle and correlates with worse survival, suggesting the involvement of melanosomes in melanoma aggression. We experimentally validated the secretion of melanosomes into surrounding tissues by melanoma tumors, which potentially affects the lethality of metastasis. We propose a simple molecular decision tree classifier for predicting a tumor's subtype based on representative genes from the three identified signatures. Key predictor genes were experimentally validated on melanoma samples taken from patients with varying survival outcomes. Our three-pattern approach for classifying melanoma tumors can contribute to advancing the understanding of melanoma variability and promote accurate diagnosis, prognostication, and treatment.
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Affiliation(s)
- Dvir Netanely
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Stav Leibou
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roma Parikh
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Neta Stern
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Hananya Vaknine
- Department of Oncology, Edith Wolfson Medical Center, Holon, Israel
| | - Ronen Brenner
- Department of Oncology, Edith Wolfson Medical Center, Holon, Israel
| | - Sarah Amar
- Department of Oncology, Edith Wolfson Medical Center, Holon, Israel
| | - Rivi Haiat Factor
- Department of Plastic and Reconstructive Surgery, Edith Wolfson Medical Center, Holon, Israel
| | - Tomer Perluk
- Department of Plastic and Reconstructive Surgery, Edith Wolfson Medical Center, Holon, Israel
| | - Jacob Frand
- Department of Plastic and Reconstructive Surgery, Edith Wolfson Medical Center, Holon, Israel
| | - Eran Nizri
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Surgery A, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Dov Hershkovitz
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Pathology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | - Carmit Levy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
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9
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Grossman D, Okwundu N, Bartlett EK, Marchetti MA, Othus M, Coit DG, Hartman RI, Leachman SA, Berry EG, Korde L, Lee SJ, Bar-Eli M, Berwick M, Bowles T, Buchbinder EI, Burton EM, Chu EY, Curiel-Lewandrowski C, Curtis JA, Daud A, Deacon DC, Ferris LK, Gershenwald JE, Grossmann KF, Hu-Lieskovan S, Hyngstrom J, Jeter JM, Judson-Torres RL, Kendra KL, Kim CC, Kirkwood JM, Lawson DH, Leming PD, Long GV, Marghoob AA, Mehnert JM, Ming ME, Nelson KC, Polsky D, Scolyer RA, Smith EA, Sondak VK, Stark MS, Stein JA, Thompson JA, Thompson JF, Venna SS, Wei ML, Swetter SM. Prognostic Gene Expression Profiling in Cutaneous Melanoma: Identifying the Knowledge Gaps and Assessing the Clinical Benefit. JAMA Dermatol 2020; 156:1004-1011. [PMID: 32725204 PMCID: PMC8275355 DOI: 10.1001/jamadermatol.2020.1729] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Importance Use of prognostic gene expression profile (GEP) testing in cutaneous melanoma (CM) is rising despite a lack of endorsement as standard of care. Objective To develop guidelines within the national Melanoma Prevention Working Group (MPWG) on integration of GEP testing into the management of patients with CM, including (1) review of published data using GEP tests, (2) definition of acceptable performance criteria, (3) current recommendations for use of GEP testing in clinical practice, and (4) considerations for future studies. Evidence Review The MPWG members and other international melanoma specialists participated in 2 online surveys and then convened a summit meeting. Published data and meeting abstracts from 2015 to 2019 were reviewed. Findings The MPWG members are optimistic about the future use of prognostic GEP testing to improve risk stratification and enhance clinical decision-making but acknowledge that current utility is limited by test performance in patients with stage I disease. Published studies of GEP testing have not evaluated results in the context of all relevant clinicopathologic factors or as predictors of regional nodal metastasis to replace sentinel lymph node biopsy (SLNB). The performance of GEP tests has generally been reported for small groups of patients representing particular tumor stages or in aggregate form, such that stage-specific performance cannot be ascertained, and without survival outcomes compared with data from the American Joint Committee on Cancer 8th edition melanoma staging system international database. There are significant challenges to performing clinical trials incorporating GEP testing with SLNB and adjuvant therapy. The MPWG members favor conducting retrospective studies that evaluate multiple GEP testing platforms on fully annotated archived samples before embarking on costly prospective studies and recommend avoiding routine use of GEP testing to direct patient management until prospective studies support their clinical utility. Conclusions and Relevance More evidence is needed to support using GEP testing to inform recommendations regarding SLNB, intensity of follow-up or imaging surveillance, and postoperative adjuvant therapy. The MPWG recommends further research to assess the validity and clinical applicability of existing and emerging GEP tests. Decisions on performing GEP testing and patient management based on these results should only be made in the context of discussion of testing limitations with the patient or within a multidisciplinary group.
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Affiliation(s)
- Douglas Grossman
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Dermatology, University of Utah, Salt Lake City
- Department of Oncological Sciences, University of Utah, Salt Lake City
| | | | - Edmund K Bartlett
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael A Marchetti
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Megan Othus
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Daniel G Coit
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rebecca I Hartman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Dermatology, Harvard Medical School, Boston, Massachusetts
| | - Sancy A Leachman
- Department of Dermatology and Knight Cancer Institute, Oregon Health & Science University, Portland
| | - Elizabeth G Berry
- Department of Dermatology and Knight Cancer Institute, Oregon Health & Science University, Portland
| | - Larissa Korde
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland
| | - Sandra J Lee
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Data Sciences, Harvard Medical School, Boston, Massachusetts
| | - Menashe Bar-Eli
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston
| | - Marianne Berwick
- Departments of Dermatology and Internal Medicine, University of New Mexico Cancer Center, University of New Mexico, Albuquerque
| | - Tawnya Bowles
- Department of Surgery, Division of Surgical Oncology, University of Utah, Salt Lake City
| | - Elizabeth I Buchbinder
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Department of Internal Medicine, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth M Burton
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Emily Y Chu
- Department of Dermatology, Perelman School of Medicine University of Pennsylvania, Philadelphia
| | | | - Julia A Curtis
- Department of Dermatology, University of Utah, Salt Lake City
| | - Adil Daud
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco
- Department of Hematology/Oncology, University of California, San Francisco
| | - Dekker C Deacon
- Department of Dermatology, University of Utah, Salt Lake City
| | - Laura K Ferris
- Department of Dermatology and University of Pittsburgh Clinical and Translational Science Institute, Pittsburgh, Pennsylvania
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Kenneth F Grossmann
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Medicine, Division of Oncology, University of Utah, Salt Lake City
| | - Siwen Hu-Lieskovan
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Medicine, Division of Oncology, University of Utah, Salt Lake City
| | - John Hyngstrom
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Surgery, Division of Surgical Oncology, University of Utah, Salt Lake City
| | - Joanne M Jeter
- Department of Internal Medicine and The Ohio State University Comprehensive Cancer Center, Columbus
| | - Robert L Judson-Torres
- Huntsman Cancer Institute, Salt Lake City, Utah
- Department of Dermatology, University of Utah, Salt Lake City
| | - Kari L Kendra
- Department of Internal Medicine and The Ohio State University Comprehensive Cancer Center, Columbus
| | - Caroline C Kim
- Department of Dermatology, Tufts Medical Center, Boston, Massachusetts
- Partners Healthcare, Newton Wellesley Dermatology Associates, Wellesley, Massachusetts
| | - John M Kirkwood
- Department of Internal Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - David H Lawson
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | | | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Ashfaq A Marghoob
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Janice M Mehnert
- Department of Medical Oncology, Robert Wood Johnson University Hospital, New Brunswick, New Jersey
- Rutgers Cancer Institute of New Jersey, New Brunswick
| | - Michael E Ming
- Department of Dermatology, Perelman School of Medicine University of Pennsylvania, Philadelphia
| | - Kelly C Nelson
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston
| | - David Polsky
- Department of Dermatology, Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, New York
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | - Eric A Smith
- Department of Pathology, University of Utah, Salt Lake City
| | - Vernon K Sondak
- Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida
- Department of Oncologic Sciences, University of South Florida Morsani College of Medicine, Tampa
| | - Mitchell S Stark
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Jennifer A Stein
- Department of Dermatology, Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, New York
| | - John A Thompson
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Oncology, University of Washington, Seattle
- Seattle Cancer Care Alliance, Seattle, Washington
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Suraj S Venna
- Inova Schar Cancer Institute, Department of Medicine, Virginia Commonwealth University, Fairfax
| | - Maria L Wei
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco
- Department of Dermatology, University of California, San Francisco
- Dermatology Service, Veterans Affairs Medical Center, San Francisco, California
| | - Susan M Swetter
- Stanford University Medical Center and Cancer Institute, Stanford, California
- Dermatology Service, Veterans Affairs Palo Alto Health Care System, Palo Alto, California
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10
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Johansson JA, Marie KL, Lu Y, Brombin A, Santoriello C, Zeng Z, Zich J, Gautier P, von Kriegsheim A, Brunsdon H, Wheeler AP, Dreger M, Houston DR, Dooley CM, Sims AH, Busch-Nentwich EM, Zon LI, Illingworth RS, Patton EE. PRL3-DDX21 Transcriptional Control of Endolysosomal Genes Restricts Melanocyte Stem Cell Differentiation. Dev Cell 2020; 54:317-332.e9. [PMID: 32652076 PMCID: PMC7435699 DOI: 10.1016/j.devcel.2020.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/06/2020] [Accepted: 06/09/2020] [Indexed: 01/22/2023]
Abstract
Melanocytes, replenished throughout life by melanocyte stem cells (MSCs), play a critical role in pigmentation and melanoma. Here, we reveal a function for the metastasis-associated phosphatase of regenerating liver 3 (PRL3) in MSC regeneration. We show that PRL3 binds to the RNA helicase DDX21, thereby restricting productive transcription by RNAPII at master transcription factor (MITF)-regulated endolysosomal vesicle genes. In zebrafish, this mechanism controls premature melanoblast expansion and differentiation from MSCs. In melanoma patients, restricted transcription of this endolysosomal vesicle pathway is a hallmark of PRL3-high melanomas. Our work presents the conceptual advance that PRL3-mediated control of transcriptional elongation is a differentiation checkpoint mechanism for activated MSCs and has clinical relevance for the activity of PRL3 in regenerating tissue and cancer.
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Affiliation(s)
- Jeanette A Johansson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Kerrie L Marie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuting Lu
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Alessandro Brombin
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Cristina Santoriello
- Stem Cell Program and Division of Hematology, Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, USA
| | - Zhiqiang Zeng
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Judith Zich
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hannah Brunsdon
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ann P Wheeler
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Marcel Dreger
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Waddington Building, King's Buildings, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Christopher M Dooley
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Max-Planck-Institute for Developmental Biology, Department ECNV, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Andrew H Sims
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology, Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, USA
| | - Robert S Illingworth
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, UK.
| | - E Elizabeth Patton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XU, UK; Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.
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11
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Jacob L, Witteveen A, Beumer I, Delahaye L, Wehkamp D, van den Akker J, Snel M, Chan B, Floore A, Bakx N, Brink G, Poncet C, Bogaerts J, Delorenzi M, Piccart M, Rutgers E, Cardoso F, Speed T, van 't Veer L, Glas A. Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial. Commun Biol 2020; 3:397. [PMID: 32719399 PMCID: PMC7385160 DOI: 10.1038/s42003-020-1111-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
Gene expression data obtained in large studies hold great promises for discovering disease signatures or subtypes through data analysis. It is also prone to technical variation, whose removal is essential to avoid spurious discoveries. Because this variation is not always known and can be confounded with biological signals, its removal is a challenging task. Here we provide a step-wise procedure and comprehensive analysis of the MINDACT microarray dataset. The MINDACT trial enrolled 6693 breast cancer patients and prospectively validated the gene expression signature MammaPrint for outcome prediction. The study also yielded a full-transcriptome microarray for each tumor. We show for the first time in such a large dataset how technical variation can be removed while retaining expected biological signals. Because of its unprecedented size, we hope the resulting adjusted dataset will be an invaluable tool to discover or test gene expression signatures and to advance our understanding of breast cancer.
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Affiliation(s)
- Laurent Jacob
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France
| | | | - Inès Beumer
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | | | | | | | | | - Bob Chan
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | - Arno Floore
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | - Niels Bakx
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | - Guido Brink
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands
| | | | | | - Mauro Delorenzi
- University Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Emiel Rutgers
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Terence Speed
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Laura van 't Veer
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands.
- Helen Diller Family Comprehensive Cancer Center, University California San Francisco, San Francisco, CA, USA.
| | - Annuska Glas
- Agendia NV/Agendia Inc, Amsterdam, The Netherlands.
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12
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Close HJ, Stead LF, Nsengimana J, Reilly KA, Droop A, Wurdak H, Mathew RK, Corns R, Newton‐Bishop J, Melcher AA, Short SC, Cook GP, Wilson EB. Expression profiling of single cells and patient cohorts identifies multiple immunosuppressive pathways and an altered NK cell phenotype in glioblastoma. Clin Exp Immunol 2020; 200:33-44. [PMID: 31784984 PMCID: PMC7066386 DOI: 10.1111/cei.13403] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is an aggressive cancer with a very poor prognosis. Generally viewed as weakly immunogenic, GBM responds poorly to current immunotherapies. To understand this problem more clearly we used a combination of natural killer (NK) cell functional assays together with gene and protein expression profiling to define the NK cell response to GBM and explore immunosuppression in the GBM microenvironment. In addition, we used transcriptome data from patient cohorts to classify GBM according to immunological profiles. We show that glioma stem-like cells, a source of post-treatment tumour recurrence, express multiple immunomodulatory cell surface molecules and are targeted in preference to normal neural progenitor cells by natural killer (NK) cells ex vivo. In contrast, GBM-infiltrating NK cells express reduced levels of activation receptors within the tumour microenvironment, with hallmarks of transforming growth factor (TGF)-β-mediated inhibition. This NK cell inhibition is accompanied by expression of multiple immune checkpoint molecules on T cells. Single-cell transcriptomics demonstrated that both tumour and haematopoietic-derived cells in GBM express multiple, diverse mediators of immune evasion. Despite this, immunome analysis across a patient cohort identifies a spectrum of immunological activity in GBM, with active immunity marked by co-expression of immune effector molecules and feedback inhibitory mechanisms. Our data show that GBM is recognized by the immune system but that anti-tumour immunity is restrained by multiple immunosuppressive pathways, some of which operate in the healthy brain. The presence of immune activity in a subset of patients suggests that these patients will more probably benefit from combination immunotherapies directed against multiple immunosuppressive pathways.
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Affiliation(s)
- H. J. Close
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
| | - L. F. Stead
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
| | - J. Nsengimana
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
| | - K. A. Reilly
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
| | - A. Droop
- MRC Medical Bioinformatics CentreUniversity of LeedsLeedsUK
| | - H. Wurdak
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
| | - R. K. Mathew
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
- Department of NeurosurgeryLeeds General InfirmaryLeedsUK
| | - R. Corns
- Department of NeurosurgeryLeeds General InfirmaryLeedsUK
| | - J. Newton‐Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
| | | | - S. C. Short
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
| | - G. P. Cook
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
| | - E. B. Wilson
- Leeds Institute of Medical Research at St James's, University of Leeds School of Medicine, St James's University HospitalLeedsUK
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13
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Thakur R, Laye JP, Lauss M, Diaz JMS, O'Shea SJ, Poźniak J, Filia A, Harland M, Gascoyne J, Randerson-Moor JA, Chan M, Mell T, Jönsson G, Bishop DT, Newton-Bishop J, Barrett JH, Nsengimana J. Transcriptomic Analysis Reveals Prognostic Molecular Signatures of Stage I Melanoma. Clin Cancer Res 2019; 25:7424-7435. [PMID: 31515461 DOI: 10.1158/1078-0432.ccr-18-3659] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/04/2019] [Accepted: 08/29/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Previously identified transcriptomic signatures have been based on primary and metastatic melanomas with relatively few American Joint Committee on Cancer (AJCC) stage I tumors, given difficulties in sampling small tumors. The advent of adjuvant therapies has highlighted the need for better prognostic and predictive biomarkers, especially for AJCC stage I and stage II disease. EXPERIMENTAL DESIGN A total of 687 primary melanoma transcriptomes were generated from the Leeds Melanoma Cohort (LMC). The prognostic value of existing signatures across all the AJCC stages was tested. Unsupervised clustering was performed, and the prognostic value of the resultant signature was compared with that of sentinel node biopsy (SNB) and tested as a biomarker in three published immunotherapy datasets. RESULTS Previous Lund and The Cancer Genome Atlas signatures predicted outcome in the LMC dataset (P = 10-8 to 10-4) but showed a significant interaction with AJCC stage (P = 0.04) and did not predict outcome in stage I tumors (P = 0.3-0.7). Consensus-based classification of the LMC dataset identified six classes that predicted outcome, notably in stage I disease. LMC class was a similar indicator of prognosis when compared with SNB, and it added prognostic value to the genes reported by Gerami and colleagues. One particular LMC class consistently predicted poor outcome in patients receiving immunotherapy in two of three tested datasets. Biological characterization of this class revealed high JUN and AXL expression and evidence of epithelial-to-mesenchymal transition. CONCLUSIONS A transcriptomic signature of primary melanoma was identified with prognostic value, including in stage I melanoma and in patients undergoing immunotherapy.
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Affiliation(s)
- Rohit Thakur
- University of Leeds School of Medicine, Leeds, United Kingdom
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, Texas
| | - Jonathan P Laye
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Martin Lauss
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | | | - Sally Jane O'Shea
- Mater Private Hospital Cork, Mahon, Cork, Ireland
- School of Medicine, University College Cork, Cork, Ireland
| | - Joanna Poźniak
- University of Leeds School of Medicine, Leeds, United Kingdom
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Anastasia Filia
- Centre for Translational Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Mark Harland
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Joanne Gascoyne
- University of Leeds School of Medicine, Leeds, United Kingdom
| | | | - May Chan
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Tracey Mell
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
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14
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Muralidhar S, Filia A, Nsengimana J, Poźniak J, O'Shea SJ, Diaz JM, Harland M, Randerson-Moor JA, Reichrath J, Laye JP, van der Weyden L, Adams DJ, Bishop DT, Newton-Bishop J. Vitamin D-VDR Signaling Inhibits Wnt/β-Catenin-Mediated Melanoma Progression and Promotes Antitumor Immunity. Cancer Res 2019; 79:5986-5998. [PMID: 31690667 DOI: 10.1158/0008-5472.can-18-3927] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/12/2019] [Accepted: 10/01/2019] [Indexed: 11/16/2022]
Abstract
1α,25-Dihydroxyvitamin D3 signals via the vitamin D receptor (VDR). Higher serum vitamin D is associated with thinner primary melanoma and better outcome, although a causal mechanism has not been established. As patients with melanoma commonly avoid sun exposure, and consequent vitamin D deficiency might worsen outcomes, we interrogated 703 primary melanoma transcriptomes to understand the role of vitamin D-VDR signaling and replicated the findings in The Cancer Genome Atlas metastases. VDR expression was independently protective for melanoma-related death in both primary and metastatic disease. High tumor VDR expression was associated with upregulation of pathways mediating antitumor immunity and corresponding with higher imputed immune cell scores and histologically detected tumor-infiltrating lymphocytes. High VDR-expressing tumors had downregulation of proliferative pathways, notably Wnt/β-catenin signaling. Deleterious low VDR levels resulted from promoter methylation and gene deletion in metastases. Vitamin D deficiency (<25 nmol/L ∼ 10 ng/mL) shortened survival in primary melanoma in a VDR-dependent manner. In vitro functional validation studies showed that elevated vitamin D-VDR signaling inhibited Wnt/β-catenin signaling genes. Murine melanoma cells overexpressing VDR produced fewer pulmonary metastases than controls in tail-vein metastasis assays. In summary, vitamin D-VDR signaling contributes to controlling pro-proliferative/immunosuppressive Wnt/β-catenin signaling in melanoma and this is associated with less metastatic disease and stronger host immune responses. This is evidence of a causal relationship between vitamin D-VDR signaling and melanoma survival, which should be explored as a therapeutic target in primary resistance to checkpoint blockade. SIGNIFICANCE: VDR expression could potentially be used as a biomarker to stratify patients with melanoma that may respond better to immunotherapy.
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Affiliation(s)
- Sathya Muralidhar
- University of Leeds School of Medicine, Leeds, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Anastasia Filia
- Centre for Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Joanna Poźniak
- University of Leeds School of Medicine, Leeds, United Kingdom
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sally J O'Shea
- University of Leeds School of Medicine, Leeds, United Kingdom
- Faculty of Medicine and Health, University College Cork, Cork, Ireland
- Mater Private Hospital Cork, Citygate, Mahon, Cork, Ireland
| | - Joey M Diaz
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Mark Harland
- University of Leeds School of Medicine, Leeds, United Kingdom
| | | | - Jörg Reichrath
- Center for Clinical and Experimental Photodermatology, The Saarland University Hospital, Homburg, Germany
| | - Jonathan P Laye
- University of Leeds School of Medicine, Leeds, United Kingdom
| | - Louise van der Weyden
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - D T Bishop
- University of Leeds School of Medicine, Leeds, United Kingdom
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15
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Travnickova J, Wojciechowska S, Khamseh A, Gautier P, Brown DV, Lefevre T, Brombin A, Ewing A, Capper A, Spitzer M, Dilshat R, Semple CA, Mathers ME, Lister JA, Steingrimsson E, Voet T, Ponting CP, Patton EE. Zebrafish MITF-Low Melanoma Subtype Models Reveal Transcriptional Subclusters and MITF-Independent Residual Disease. Cancer Res 2019; 79:5769-5784. [PMID: 31582381 DOI: 10.1158/0008-5472.can-19-0037] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 06/28/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022]
Abstract
The melanocyte-inducing transcription factor (MITF)-low melanoma transcriptional signature is predictive of poor outcomes for patients, but little is known about its biological significance, and animal models are lacking. Here, we used zebrafish genetic models with low activity of Mitfa (MITF-low) and established that the MITF-low state is causal of melanoma progression and a predictor of melanoma biological subtype. MITF-low zebrafish melanomas resembled human MITF-low melanomas and were enriched for stem and invasive (mesenchymal) gene signatures. MITF-low activity coupled with a p53 mutation was sufficient to promote superficial growth melanomas, whereas BRAFV600E accelerated MITF-low melanoma onset and further promoted the development of MITF-high nodular growth melanomas. Genetic inhibition of MITF activity led to rapid regression; recurrence occurred following reactivation of MITF. At the regression site, there was minimal residual disease that was resistant to loss of MITF activity (termed MITF-independent cells) with very low-to-no MITF activity or protein. Transcriptomic analysis of MITF-independent residual disease showed enrichment of mesenchymal and neural crest stem cell signatures similar to human therapy-resistant melanomas. Single-cell RNA sequencing revealed MITF-independent residual disease was heterogeneous depending on melanoma subtype. Further, there was a shared subpopulation of residual disease cells that was enriched for a neural crest G0-like state that preexisted in the primary tumor and remained present in recurring melanomas. These findings suggest that invasive and stem-like programs coupled with cellular heterogeneity contribute to poor outcomes for MITF-low melanoma patients and that MITF-independent subpopulations are an important therapeutic target to achieve long-term survival outcomes. SIGNIFICANCE: This study provides a useful model for MITF-low melanomas and MITF-independent cell populations that can be used to study the mechanisms that drive these tumors as well as identify potential therapeutic options.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/22/5769/F1.large.jpg.
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Affiliation(s)
- Jana Travnickova
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom.,CRUK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sonia Wojciechowska
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom.,CRUK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ava Khamseh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom.,Higgs Centre for Theoretical Physics, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel V Brown
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium.,Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Thomas Lefevre
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
| | - Alessandro Brombin
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom.,CRUK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ailith Ewing
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Amy Capper
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom.,CRUK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Michaela Spitzer
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom; and European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ramile Dilshat
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Colin A Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Marie E Mathers
- Department of Pathology, Western General Hospital, Edinburgh, United Kingdom
| | - James A Lister
- Department of Human and Molecular Genetics and Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Eiríkur Steingrimsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Thierry Voet
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Chris P Ponting
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - E Elizabeth Patton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. .,CRUK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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16
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Poźniak J, Nsengimana J, Laye JP, O'Shea SJ, Diaz JMS, Droop AP, Filia A, Harland M, Davies JR, Mell T, Randerson-Moor JA, Muralidhar S, Hogan SA, Freiberger SN, Levesque MP, Cook GP, Bishop DT, Newton-Bishop J. Genetic and Environmental Determinants of Immune Response to Cutaneous Melanoma. Cancer Res 2019; 79:2684-2696. [PMID: 30773503 PMCID: PMC6544535 DOI: 10.1158/0008-5472.can-18-2864] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/16/2018] [Accepted: 01/25/2019] [Indexed: 01/05/2023]
Abstract
The immune response to melanoma improves the survival in untreated patients and predicts the response to immune checkpoint blockade. Here, we report genetic and environmental predictors of the immune response in a large primary cutaneous melanoma cohort. Bioinformatic analysis of 703 tumor transcriptomes was used to infer immune cell infiltration and to categorize tumors into immune subgroups, which were then investigated for association with biological pathways, clinicopathologic factors, and copy number alterations. Three subgroups, with "low", "intermediate", and "high" immune signals, were identified in primary tumors and replicated in metastatic tumors. Genes in the low subgroup were enriched for cell-cycle and metabolic pathways, whereas genes in the high subgroup were enriched for IFN and NF-κB signaling. We identified high MYC expression partially driven by amplification, HLA-B downregulation, and deletion of IFNγ and NF-κB pathway genes as the regulators of immune suppression. Furthermore, we showed that cigarette smoking, a globally detrimental environmental factor, modulates immunity, reducing the survival primarily in patients with a strong immune response. Together, these analyses identify a set of factors that can be easily assessed that may serve as predictors of response to immunotherapy in patients with melanoma. SIGNIFICANCE: These findings identify novel genetic and environmental modulators of the immune response against primary cutaneous melanoma and predict their impact on patient survival.See related commentary by Anichini, p. 2457.
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Affiliation(s)
- Joanna Poźniak
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom.
| | - Jérémie Nsengimana
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Jonathan P Laye
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Sally J O'Shea
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
- Faculty of Medicine and Health, University College Cork, Cork, Ireland
- Mater Private Hospital Cork, Citygate, Mahon, Cork, Ireland
| | - Joey Mark S Diaz
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Alastair P Droop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
- Medical Research Council (MRC) Medical Bioinformatics Centre, University of Leeds, Leeds, United Kingdom
| | - Anastasia Filia
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
- Centre for Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Mark Harland
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - John R Davies
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Tracey Mell
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | | | - Sathya Muralidhar
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Sabrina A Hogan
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zürich, Switzerland
| | - Sandra Nicole Freiberger
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zürich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zürich Hospital, University of Zürich, Zürich, Switzerland
| | - Graham P Cook
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Julia Newton-Bishop
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
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17
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Keller J, Schwartz TL, Lizalek JM, Chang E, Patel AD, Hurley MY, Hsueh EC. Prospective validation of the prognostic 31-gene expression profiling test in primary cutaneous melanoma. Cancer Med 2019; 8:2205-2212. [PMID: 30950242 PMCID: PMC6536922 DOI: 10.1002/cam4.2128] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/27/2019] [Accepted: 03/13/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Gene expression profiling (GEP) has been integrated into cancer treatment decision-making in multiple neoplasms. We prospectively evaluated the prognostic utility of the 31-GEP test (DecisionDx-Melanoma, Castle Biosciences, Inc) in cutaneous melanoma (CM) patients undergoing sentinel node biopsy (SNB). METHODS One hundred fifty-nine patients (age 26-88) diagnosed with melanoma between 01/2013 and 8/2015 underwent SNB and concurrent GEP testing. GEP results were reported as low-risk Class 1 (subclasses 1A and 1B) or high-risk Class 2 (subclasses 2A and 2B). Statistical analyses were performed with chi-square analysis, t tests, log-rank tests, and Cox proportional hazard models. Recurrence-free survival (RFS) and distant metastasis-free survival (DMFS) were estimated using Kaplan-Meier method. RESULTS Median follow-up was 44.9 months for event-free cases. Median Breslow thickness was 1.4 mm (0.2-15.0 mm). There were 117 Class 1 and 42 Class 2 patients. Gender, age, Breslow thickness, ulceration, SNB positivity, and AJCC stage were significantly associated with GEP classification (P < 0.05 for all). Recurrence and distant metastasis rates were 5% and 1% for Class 1 patients compared with 55% and 36% for Class 2 patients. Sensitivities of Class 2 and SNB for recurrence were 79% and 34%, respectively. Of 10 SNB-positive/Class 2 patients, 9 recurred. By multivariate analysis, only SNB result and GEP class were statistically associated with both RFS (P = 0.008 and 0.0001) and DMFS (P = 0.019 and 0.001). CONCLUSIONS Gene expression profiling Class 2 result and SNB positivity were independently associated with recurrence and distant metastasis in primary CM patients. GEP testing may have additive prognostic utility in initial staging work-up of these patients.
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Affiliation(s)
- Jennifer Keller
- Department of SurgerySaint Louis UniversitySt. LouisMissouri
| | | | | | - Ea‐sle Chang
- Department of SurgerySaint Louis UniversitySt. LouisMissouri
| | - Ashaki D. Patel
- Department of SurgerySaint Louis UniversitySt. LouisMissouri
| | - Maria Y. Hurley
- Department of DermatologySaint Louis UniversitySt. LouisMissouri
| | - Eddy C. Hsueh
- Department of SurgerySaint Louis UniversitySt. LouisMissouri
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18
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Bowlt Blacklock KL, Birand Z, Selmic LE, Nelissen P, Murphy S, Blackwood L, Bass J, McKay J, Fox R, Beaver S, Starkey M. Genome-wide analysis of canine oral malignant melanoma metastasis-associated gene expression. Sci Rep 2019; 9:6511. [PMID: 31019223 PMCID: PMC6482147 DOI: 10.1038/s41598-019-42839-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/04/2019] [Indexed: 12/12/2022] Open
Abstract
Oral malignant melanoma (OMM) is the most common canine melanocytic neoplasm. Overlap between the somatic mutation profiles of canine OMM and human mucosal melanomas suggest a shared UV-independent molecular aetiology. In common with human mucosal melanomas, most canine OMM metastasise. There is no reliable means of predicting canine OMM metastasis, and systemic therapies for metastatic disease are largely palliative. Herein, we employed exon microarrays for comparative expression profiling of FFPE biopsies of 18 primary canine OMM that metastasised and 10 primary OMM that did not metastasise. Genes displaying metastasis-associated expression may be targets for anti-metastasis treatments, and biomarkers of OMM metastasis. Reduced expression of CXCL12 in the metastasising OMMs implies that the CXCR4/CXCL12 axis may be involved in OMM metastasis. Increased expression of APOBEC3A in the metastasising OMMs may indicate APOBEC3A-induced double-strand DNA breaks and pro-metastatic hypermutation. DNA double strand breakage triggers the DNA damage response network and two Fanconi anaemia DNA repair pathway members showed elevated expression in the metastasising OMMs. Cross-validation was employed to test a Linear Discriminant Analysis classifier based upon the RT-qPCR-measured expression levels of CXCL12, APOBEC3A and RPL29. Classification accuracies of 94% (metastasising OMMs) and 86% (non-metastasising OMMs) were estimated.
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Affiliation(s)
| | - Z Birand
- Animal Health Trust, Newmarket, Suffolk, UK
| | - L E Selmic
- Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA
| | - P Nelissen
- Dick White Referrals, Newmarket, Suffolk, UK
| | - S Murphy
- Animal Health Trust, Newmarket, Suffolk, UK
- The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - L Blackwood
- Institute of Veterinary Science, University of Liverpool, Liverpool, UK
| | - J Bass
- Animal Health Trust, Newmarket, Suffolk, UK
- Finn Pathologists, Harleston, UK
| | - J McKay
- IDEXX Laboratories, Ltd, Wetherby, UK
| | - R Fox
- Finn Pathologists, Harleston, UK
| | - S Beaver
- Nationwide Laboratory Services, Poulton-le-Fylde, UK
| | - M Starkey
- Animal Health Trust, Newmarket, Suffolk, UK.
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19
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Identification of gene expression levels in primary melanoma associated with clinically meaningful characteristics. Melanoma Res 2019; 28:380-389. [PMID: 29975213 DOI: 10.1097/cmr.0000000000000473] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Factors influencing melanoma survival include sex, age, clinical stage, lymph node involvement, as well as Breslow thickness, presence of tumor-infiltrating lymphocytes based on histological analysis of primary melanoma, mitotic rate, and ulceration. Identification of genes whose expression in primary tumors is associated with these key tumor/patient characteristics can shed light on molecular mechanisms of melanoma survival. Here, we show results from a gene expression analysis of formalin-fixed paraffin-embedded primary melanomas with extensive clinical annotation. The Cancer Genome Atlas data on primary melanomas were used for validation of nominally significant associations. We identified five genes that were significantly associated with the presence of tumor-infiltrating lymphocytes in the joint analysis after adjustment for multiple testing: IL1R2, PPL, PLA2G3, RASAL1, and SGK2. We also identified two genes significantly associated with melanoma metastasis to the regional lymph nodes (PIK3CG and IL2RA), and two genes significantly associated with sex (KDM5C and KDM6A). We found that LEF1 was significantly associated with Breslow thickness and CCNA2 and UBE2T with mitosis. RAD50 was the gene most significantly associated with survival, with a higher level of expression associated with worse survival.
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20
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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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21
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Comparison of melanoma gene expression score with histopathology, fluorescence in situ hybridization, and SNP array for the classification of melanocytic neoplasms. Mod Pathol 2018; 31:1733-1743. [PMID: 29955141 PMCID: PMC6631355 DOI: 10.1038/s41379-018-0087-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/03/2018] [Accepted: 05/13/2018] [Indexed: 12/12/2022]
Abstract
While most melanomas can be distinguished from nevi by histopathology, the histology is ambiguous for some melanocytic tumors, contributing to diagnostic uncertainty. Therefore molecular assays, including FISH or SNP array, and more recently a gene expression test (myPath, Myriad Genetics) have been proposed to aid in the work-up of ambiguous tumors. Two hundred and sixty-eight prospectively submitted cases were gathered, with the goal of comparing the myPath assay to morphologic diagnosis in (1) morphologically unequivocal cases (198), and to morphologic diagnosis and FISH in (2) morphologically ambiguous cases (70). Melanoma FISH was performed using probes for 6p25, 6q23, 11q13, Cep6, 9p21, and Cep9 and scored according to established criteria. The myPath assay was scored by the manufacturer as benign, indeterminate, or malignant. In the unequivocal group, myPath assay showed 75% agreement with morphologic diagnosis, with 67% sensitivity and 81% specificity. In the ambiguous group, FISH and myPath showed 69% inter-test agreement. For these cases agreement with histopathologic interpretation was 84% for FISH and 74% for myPath. Sensitivity and specificity of FISH was 61 and 100%, 50 and 93% for myPath, respectively. Cases from both groups in which myPath was discordant with either morphologic diagnosis and/or FISH (81/268 cases), were submitted for evaluation by two experienced dermatopathologist and also by SNP-array. SNP-array results correlated better than FISH, which correlated better than myPath, with the morphologic interpretation. Our findings document that molecular diagnostics show good correlation with consensus diagnoses, but discordant results occur, and vary in level of correlation with consensus interpretations. Studies with long-term outcomes data within specific ambiguous lesion subsets are required to establish the accuracy of this test, as each molecular diagnostic technique has limitations based on both lack of clinical outcomes data in ambiguous melanocytic tumors and in terms of their sensitivity and specificity in melanocytic lesion subtypes.
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22
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Lipplaa A, Fernandes R, Marshall A, Lorigan P, Dunn J, Myers KA, Barker E, Newton-Bishop J, Middleton MR, Corrie PG. 25-hydroxyvitamin D serum levels in patients with high risk resected melanoma treated in an adjuvant bevacizumab trial. Br J Cancer 2018; 119:793-800. [PMID: 30033445 PMCID: PMC6189120 DOI: 10.1038/s41416-018-0179-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 06/14/2018] [Accepted: 06/20/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Studies evaluating a relationship of vitamin D in patients with primary melanoma have consistently identified an inverse correlation with Breslow thickness, but an inconsistent impact on survival. Vitamin D in later stages of melanoma has been less studied. METHODS Vitamin D was measured in serum from 341 patients with resected stage IIB-IIIC melanoma recruited to the AVAST-M adjuvant melanoma randomised trial, collected prior to randomisation, then at 3 and 12 months. Vitamin D levels were compared with patient demographics, known melanoma prognostic factors, disease-free interval (DFI) and overall survival (OS). RESULTS A total of 73% patients had stage III melanoma, 32% were enroled (and therefore tested) >1 year after primary melanoma diagnosis. Median pre-randomisation vitamin D level was 56.5 (range 12.6-189.0 nmol/L). Vitamin D levels did not significantly vary over 12 months (p = 0.24). Individual pre-randomisation vitamin D levels did not differ significantly for Breslow thickness, tumour ulceration, or disease stage. Neither did pre-randomisation vitamin D predict for DFI (HR = 0.98 per 10 nmol/L increase; 95% confidence interval (CI) 0.93-1.04, p = 0.59) or OS (HR = 0.96 per 10 nmol/L increase, 95% CI 0.90-1.03, p = 0.31). For stage II patients, DFI improved with higher pre-randomisation vitamin D levels for those on bevacizumab (HR = 0.74 per 10 nmol nmol/L increase; 95% CI 0.56-0.97), but not for the observation arm (HR = 1.07 per 10 nmol/L increase; 95% CI 0.85-1.34). CONCLUSIONS In this stage II/III melanoma cohort, vitamin D did not correlate with known prognostic markers, nor predict for DFI or OS, but there was some evidence of benefit for patients with stage II disease treated with bevacizumab.
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Affiliation(s)
- Astrid Lipplaa
- Department of Oncology, University of Oxford, CB2 0QQ, Oxford, United Kingdom
- Leiden University Medical Center, Leiden, The Netherlands
| | - Ricardo Fernandes
- Department of Oncology, University of Oxford, CB2 0QQ, Oxford, United Kingdom
- Division of Medical Oncology, Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Andrea Marshall
- Warwick Clinical Trials Unit, University of Warwick, CV4 7AL, Coventry, United Kingdom
| | - Paul Lorigan
- University of Manchester and Christie NHS Foundation Trust, M20 4BX, Manchester, United Kingdom
| | - Janet Dunn
- Warwick Clinical Trials Unit, University of Warwick, CV4 7AL, Coventry, United Kingdom
| | - Kevin A Myers
- Department of Oncology, University of Oxford, CB2 0QQ, Oxford, United Kingdom
- Experimental Cancer Medicine Centre, OX3 7DQ, Oxford, United Kingdom
| | - Emily Barker
- Cambridge Cancer Trials Centre, Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ, Cambridge, United Kingdom
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, LS9 7TF, Leeds, United Kingdom
| | - Mark R Middleton
- Department of Oncology, University of Oxford, CB2 0QQ, Oxford, United Kingdom.
- NIHR Biomedical Research Centre, OX3 7LE, Oxford, United Kingdom.
| | - Pippa G Corrie
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ, Cambridge, United Kingdom
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23
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Miskolczi Z, Smith MP, Rowling EJ, Ferguson J, Barriuso J, Wellbrock C. Collagen abundance controls melanoma phenotypes through lineage-specific microenvironment sensing. Oncogene 2018; 37:3166-3182. [PMID: 29545604 PMCID: PMC5992128 DOI: 10.1038/s41388-018-0209-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/16/2018] [Accepted: 02/13/2018] [Indexed: 01/15/2023]
Abstract
Despite the general focus on an invasive and de-differentiated phenotype as main driver of cancer metastasis, in melanoma patients many metastatic lesions display a high degree of pigmentation, indicative for a differentiated phenotype. Indeed, studies in mice and fish show that melanoma cells switch to a differentiated phenotype at secondary sites, possibly because in melanoma differentiation is closely linked to proliferation through the lineage-specific transcriptional master regulator MITF. Importantly, while a lot of effort has gone into identifying factors that induce the de-differentiated/invasive phenotype, it is not well understood how the switch to the differentiated/proliferative phenotype is controlled. We identify collagen as a contributor to this switch. We demonstrate that collagen stiffness induces melanoma differentiation through a YAP/PAX3/MITF axis and show that in melanoma patients increased collagen abundance correlates with nuclear YAP localization. However, the interrogation of large patient datasets revealed that in the context of the tumour microenvironment, YAP function is more complex. In the absence of fibroblasts, YAP/PAX3-mediated transcription prevails, but in the presence of fibroblasts tumour growth factor-β suppresses YAP/PAX3-mediated MITF expression and induces YAP/TEAD/SMAD-driven transcription and a de-differentiated phenotype. Intriguingly, while high collagen expression is correlated with poorer patient survival, the worst prognosis is seen in patients with high collagen expression, who also express MITF target genes such as the differentiation markers TRPM1, TYR and TYRP1, as well as CDK4. In summary, we reveal a distinct lineage-specific route of YAP signalling that contributes to the regulation of melanoma pigmentation and uncovers a set of potential biomarkers predictive for poor survival.
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Affiliation(s)
- Zsofia Miskolczi
- Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, School of Medical Sciences, Division of Cancer Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Michael P Smith
- Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, School of Medical Sciences, Division of Cancer Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Emily J Rowling
- Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, School of Medical Sciences, Division of Cancer Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Jennifer Ferguson
- Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, School of Medical Sciences, Division of Cancer Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Jorge Barriuso
- Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, School of Medical Sciences, Division of Cancer Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Claudia Wellbrock
- Manchester Cancer Research Centre, Faculty of Biology, Medicine and Health, School of Medical Sciences, Division of Cancer Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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24
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Nsengimana J, Laye J, Filia A, O’Shea S, Muralidhar S, Poźniak J, Droop A, Chan M, Walker C, Parkinson L, Gascoyne J, Mell T, Polso M, Jewell R, Randerson-Moor J, Cook GP, Bishop DT, Newton-Bishop J. β-Catenin-mediated immune evasion pathway frequently operates in primary cutaneous melanomas. J Clin Invest 2018; 128:2048-2063. [PMID: 29664013 PMCID: PMC5919828 DOI: 10.1172/jci95351] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/27/2018] [Indexed: 12/19/2022] Open
Abstract
Immunotherapy prolongs survival in only a subset of melanoma patients, highlighting the need to better understand the driver tumor microenvironment. We conducted bioinformatic analyses of 703 transcriptomes to probe the immune landscape of primary cutaneous melanomas in a population-ascertained cohort. We identified and validated 6 immunologically distinct subgroups, with the largest having the lowest immune scores and the poorest survival. This poor-prognosis subgroup exhibited expression profiles consistent with β-catenin-mediated failure to recruit CD141+ DCs. A second subgroup displayed an equally bad prognosis when histopathological factors were adjusted for, while 4 others maintained comparable survival profiles. The 6 subgroups were replicated in The Cancer Genome Atlas (TCGA) melanomas, where β-catenin signaling was also associated with low immune scores predominantly related to hypomethylation. The survival benefit of high immune scores was strongest in patients with double-WT tumors for BRAF and NRAS, less strong in BRAF-V600 mutants, and absent in NRAS (codons 12, 13, 61) mutants. In summary, we report evidence for a β-catenin-mediated immune evasion in 42% of melanoma primaries overall and in 73% of those with the worst outcome. We further report evidence for an interaction between oncogenic mutations and host response to melanoma, suggesting that patient stratification will improve immunotherapeutic outcomes.
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Affiliation(s)
- Jérémie Nsengimana
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Jon Laye
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Anastasia Filia
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Sally O’Shea
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Sathya Muralidhar
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Joanna Poźniak
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Alastair Droop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
- Medical Research Council (MRC) Medical Bioinformatics Centre, University of Leeds, Leeds, United Kingdom
| | - May Chan
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Christy Walker
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Louise Parkinson
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Joanne Gascoyne
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Tracey Mell
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Minttu Polso
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Rosalyn Jewell
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | | | - Graham P. Cook
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - D. Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Julia Newton-Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
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25
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Yang S, Xu J, Zeng X. A six-long non-coding RNA signature predicts prognosis in melanoma patients. Int J Oncol 2018; 52:1178-1188. [PMID: 29436619 PMCID: PMC5843393 DOI: 10.3892/ijo.2018.4268] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/10/2018] [Indexed: 12/20/2022] Open
Abstract
The aim of this study was to identify long non-coding RNAs (lncRNAs) which may prove useful for risk-classifying patients with melanoma. For this purpose, based on a dataset from The Cancer Genome Atlas (TCGA), we selected and analyzed samples from melanoma stages I, II, III and IV, from which differentially expressed lncRNAs were identified. The lncRNAs were classified using two-way hierarchical clustering analysis and analysis of support vector machine (SVM), followed by Kaplan-Meier survival analysis. The prognostic capacity of the signature was verified on an independent dataset. lncRNA-mRNA networks were built using signature lncRNAs and corresponding target genes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was conducted on the target genes. A total of 48 differentially expressed lncRNAs were identified, from which 6 signature lncRNAs (AL050303 and LINC00707, LINC01324, RP11-85G21, RP4-794I6.4 and RP5-855F16) were identified. Two-way hierarchical clustering analysis revealed that the accuracy of the six-lncRNA signature in risk-stratifying samples was 84.84%, and the accuracy of the SVM classifier was 85.9%. This predictive signature performed well on the validation dataset [accuracy, 86.76; area under the ROC curve (AUROC), 0.816]. A total of 720 target genes of the 6 lncRNAs were selected for the lncRNA-mRNA networks. These genes were significantly related to mitogen-activated protein kinase (MAPK), the neurotrophin signaling pathway, focal adhesion pathways, and several immune and inflammation-related pathways. On the whole, we identified a six-lncRNA prognostic signature for risk-stratifying patients with melanoma. These lncRNAs may affect prognosis by regulating the MAPK pathway, immune and inflammation-related pathways, the neurotrophin signaling pathway and focal adhesion pathways.
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Affiliation(s)
- Shuocheng Yang
- Department of Medical Cosmetology, Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai 200072, P.R. China
| | - Jianguo Xu
- Department of Plastic Surgery, Changhai Hospital, Shanghai 200433, P.R. China
| | - Xuan Zeng
- Department of Plastic and Reconstructive Surgery, Guangzhou General Hospital of Guangzhou Military Command, Guangzhou, Guangdong 510010, P.R. China
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26
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Branca M, Orso S, Molinari RC, Xu H, Guerrier S, Zhang Y, Mili N. Is nonmetastatic cutaneous melanoma predictable through genomic biomarkers? Melanoma Res 2018; 28:21-29. [PMID: 29194095 DOI: 10.1097/cmr.0000000000000412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cutaneous melanoma is a highly aggressive skin cancer whose treatment and prognosis are critically affected by the presence of metastasis. In this study, we address the following issue: which gene transcripts and what kind of interactions between them can allow to predict nonmetastatic from metastatic melanomas with a high level of accuracy? We carry out a meta-analysis on the first gene expression set of the Leeds melanoma cohort, as made available online on 11 May 2016 through the ArrayExpress platform with MicroArray Gene Expression number 4725. According to the authors, primary melanoma mRNA expression was measured in 204 tumours using an illumina DASL HT12 4 whole-genome array. The tumour transcripts were selected through a recently proposed predictive-based regression algorithm for gene-network selection. A set of 64 equivalent models, each including only two gene transcripts, were each sufficient to accurately classify primary tumours into metastatic and nonmetastatic melanomas. The sensitivity and specificity of the genomic-based models were, respectively, 4% (95% confidence interval: 0.11-21.95%) and 99% (95% confidence interval: 96.96-99.99%). The very high specificity coupled with a significantly large positive likelihood ratio leads to a conclusive increase in the likelihood of disease when these biomarkers are present in the primary tumour. In conjunction with other highly sensitive methods, this approach can aspire to be part of the future standard diagnosis methods for the screening of metastatic cutaneous melanoma. The small dimension of the selected transcripts models enables easy handling of large-scale genomic testing procedures. Moreover, some of the selected transcripts have an understandable link with what is known about cutaneous melanoma oncogenesis, opening a window on the molecular pathways underlying the metastatic process of this disease.
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Affiliation(s)
- Mattia Branca
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, Geneva, Switzerland
| | - Samuel Orso
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, Geneva, Switzerland
| | - Roberto C Molinari
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, Geneva, Switzerland
| | - Haotian Xu
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, Geneva, Switzerland
| | - Stéphane Guerrier
- Department of Statistics and Institute for CyberScience, Eberly College of Science, Pennsylvania State University, State College, Pennsylvania, USA
| | - Yuming Zhang
- Department of Statistics and Institute for CyberScience, Eberly College of Science, Pennsylvania State University, State College, Pennsylvania, USA
| | - Nabil Mili
- Research Center for Statistics, Geneva School of Economics and Management, University of Geneva, Geneva, Switzerland
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Del Castillo Velasco‐Herrera M, van der Weyden L, Nsengimana J, Speak AO, Sjöberg MK, Bishop DT, Jönsson G, Newton‐Bishop J, Adams DJ. Comparative genomics reveals that loss of lunatic fringe (LFNG) promotes melanoma metastasis. Mol Oncol 2018; 12:239-255. [PMID: 29193607 PMCID: PMC5792739 DOI: 10.1002/1878-0261.12161] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/16/2017] [Accepted: 11/07/2017] [Indexed: 12/17/2022] Open
Abstract
Metastasis is the leading cause of death in patients with advanced melanoma, yet the somatic alterations that aid tumour cell dissemination and colonisation are poorly understood. Here, we deploy comparative genomics to identify and validate clinically relevant drivers of melanoma metastasis. To do this, we identified a set of 976 genes whose expression level was associated with a poor outcome in patients from two large melanoma cohorts. Next, we characterised the genomes and transcriptomes of mouse melanoma cell lines defined as weakly metastatic, and their highly metastatic derivatives. By comparing expression data between species, we identified lunatic fringe (LFNG), among 28 genes whose expression level is predictive of poor prognosis and whose altered expression is associated with a prometastatic phenotype in mouse melanoma cells. CRISPR/Cas9-mediated knockout of Lfng dramatically enhanced the capability of weakly metastatic melanoma cells to metastasise in vivo, a phenotype that could be rescued with the Lfng cDNA. Notably, genomic alterations disrupting LFNG are found exclusively in human metastatic melanomas sequenced as part of The Cancer Genome Atlas. Using comparative genomics, we show that LFNG expression plays a functional role in regulating melanoma metastasis.
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Affiliation(s)
| | | | - Jeremie Nsengimana
- Leeds Institute of Cancer and PathologySt James's University HospitalUniversity of LeedsUK
| | - Anneliese O. Speak
- Experimental Cancer GeneticsWellcome Trust Sanger InstituteHinxtonCambridgeUK
| | - Marcela K. Sjöberg
- Experimental Cancer GeneticsWellcome Trust Sanger InstituteHinxtonCambridgeUK
- Departamento de Biología Celular y MolecularFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - David Timothy Bishop
- Leeds Institute of Cancer and PathologySt James's University HospitalUniversity of LeedsUK
| | - Göran Jönsson
- Division of Oncology and PathologyDepartment of Clinical SciencesSkåne University HospitalLund UniversitySweden
| | - Julia Newton‐Bishop
- Leeds Institute of Cancer and PathologySt James's University HospitalUniversity of LeedsUK
| | - David J. Adams
- Experimental Cancer GeneticsWellcome Trust Sanger InstituteHinxtonCambridgeUK
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28
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Metri R, Mohan A, Nsengimana J, Pozniak J, Molina-Paris C, Newton-Bishop J, Bishop D, Chandra N. Identification of a gene signature for discriminating metastatic from primary melanoma using a molecular interaction network approach. Sci Rep 2017; 7:17314. [PMID: 29229936 PMCID: PMC5725601 DOI: 10.1038/s41598-017-17330-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/10/2017] [Indexed: 01/15/2023] Open
Abstract
Understanding the biological factors that are characteristic of metastasis in melanoma remains a key approach to improving treatment. In this study, we seek to identify a gene signature of metastatic melanoma. We configured a new network-based computational pipeline, combined with a machine learning method, to mine publicly available transcriptomic data from melanoma patient samples. Our method is unbiased and scans a genome-wide protein-protein interaction network using a novel formulation for network scoring. Using this, we identify the most influential, differentially expressed nodes in metastatic as compared to primary melanoma. We evaluated the shortlisted genes by a machine learning method to rank them by their discriminatory capacities. From this, we identified a panel of 6 genes, ALDH1A1, HSP90AB1, KIT, KRT16, SPRR3 and TMEM45B whose expression values discriminated metastatic from primary melanoma (87% classification accuracy). In an independent transcriptomic data set derived from 703 primary melanomas, we showed that all six genes were significant in predicting melanoma specific survival (MSS) in a univariate analysis, which was also consistent with AJCC staging. Further, 3 of these genes, HSP90AB1, SPRR3 and KRT16 remained significant predictors of MSS in a joint analysis (HR = 2.3, P = 0.03) although, HSP90AB1 (HR = 1.9, P = 2 × 10-4) alone remained predictive after adjusting for clinical predictors.
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Affiliation(s)
- Rahul Metri
- IISc Mathematics Initiative (IMI), Indian Institute of Science, Bangalore, Karnataka, India
| | - Abhilash Mohan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Joanna Pozniak
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Carmen Molina-Paris
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - David Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Nagasuma Chandra
- IISc Mathematics Initiative (IMI), Indian Institute of Science, Bangalore, Karnataka, India.
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.
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29
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Testa U, Castelli G, Pelosi E. Melanoma: Genetic Abnormalities, Tumor Progression, Clonal Evolution and Tumor Initiating Cells. Med Sci (Basel) 2017; 5:E28. [PMID: 29156643 PMCID: PMC5753657 DOI: 10.3390/medsci5040028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/31/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022] Open
Abstract
Melanoma is an aggressive neoplasia issued from the malignant transformation of melanocytes, the pigment-generating cells of the skin. It is responsible for about 75% of deaths due to skin cancers. Melanoma is a phenotypically and molecularly heterogeneous disease: cutaneous, uveal, acral, and mucosal melanomas have different clinical courses, are associated with different mutational profiles, and possess distinct risk factors. The discovery of the molecular abnormalities underlying melanomas has led to the promising improvement of therapy, and further progress is expected in the near future. The study of melanoma precursor lesions has led to the suggestion that the pathway of tumor evolution implies the progression from benign naevi, to dysplastic naevi, to melanoma in situ and then to invasive and metastatic melanoma. The gene alterations characterizing melanomas tend to accumulate in these precursor lesions in a sequential order. Studies carried out in recent years have, in part, elucidated the great tumorigenic potential of melanoma tumor cells. These findings have led to speculation that the cancer stem cell model cannot be applied to melanoma because, in this malignancy, tumor cells possess an intrinsic plasticity, conferring the capacity to initiate and maintain the neoplastic process to phenotypically different tumor cells.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
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30
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Keller J, Diggs LP, Hsueh EC. Prognostic molecular testing in melanoma: ready for prime time? Melanoma Manag 2017; 4:171-174. [PMID: 30190922 DOI: 10.2217/mmt-2017-0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/16/2017] [Indexed: 01/02/2023] Open
Affiliation(s)
- Jennifer Keller
- Department of Surgery, Saint Louis University, St Louis, MO, USA
| | - Laurence P Diggs
- Department of Surgery, Saint Louis University, St Louis, MO, USA
| | - Eddy C Hsueh
- Department of Surgery, Saint Louis University, St Louis, MO, USA
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31
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Lin JX, Chen XW, Chen ZH, Huang XY, Yang JJ, Xing YF, Yin LH, Li X, Wu XY. A multidisciplinary team approach for nutritional interventions conducted by specialist nurses in patients with advanced colorectal cancer undergoing chemotherapy: A clinical trial. Medicine (Baltimore) 2017; 96:e7373. [PMID: 28658162 PMCID: PMC5500084 DOI: 10.1097/md.0000000000007373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND & AIMS Nutritional interventions for malnutrition in cancer patients can be helpful. However, concise intervention recommendations remain controversial. Thus, the aim of this study was to report on a nutrition intervention conducted by a multidisciplinary team of specialist nurses and to explore the effect of nutritional intervention on cancer patients. METHODS This prospective clinical trial study enrolled 110 colorectal cancer patients undergoing chemotherapy. The patients were evaluated upon admission using the 2002 Nutritional Risk Screening system (NRS-2002). The patients were randomly divided into intervention and control groups including 55 patients each. Patients in the control group were administered a normal diet, while those in the intervention group received individual recipes developed by a team of professional nurses, clinical doctors, dietitian, family caregivers, and the patients themselves. Patient weight and serum albumin and prealbumin levels were compared between the 2 groups at different time points. RESULTS There was a significant difference in patient weight and serum albumin and prealbumin levels before and after nutrition intervention in the intervention group (P < .05). In the control group, weight did not change during ordinary diet guidance. Serum albumin level was slightly improved after 12 cycles of chemotherapy, similar to the prealbumin results. There were statistically significant differences in serum albumin and prealbumin levels between the intervention and control groups after nutrition intervention (P < .05). However, there was no statistically significant difference in weight between the groups after nutrition intervention (P > .05). CONCLUSION A multidisciplinary team approach for nutrition intervention conducted by specialist nurses improved prealbumin levels in colorectal cancer patients undergoing chemotherapy, with no weight change.
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Affiliation(s)
- Jin-Xiang Lin
- Department of Medical Oncology and Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University
| | - Xiang-Wei Chen
- Department of Medical Oncology and Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University
| | - Zhan-Hong Chen
- Department of Medical Oncology and Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University
| | - Xiu-Yan Huang
- Department of Medical Oncology and Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University
| | - Jin-Jie Yang
- Department of Medical Oncology and Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University
| | - Yan-Fang Xing
- Department of Nephrology, the Third Affiliated Hospital of Guangzhou Medical University
| | - Liang-Hong Yin
- Department of Nephrology, First Affiliated Hospital of Jinan University, Guangzhou, People's Republic of China
| | - Xing Li
- Department of Medical Oncology and Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University
| | - Xiang-Yuan Wu
- Department of Medical Oncology and Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University
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32
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Badal B, Solovyov A, Di Cecilia S, Chan JM, Chang LW, Iqbal R, Aydin IT, Rajan GS, Chen C, Abbate F, Arora KS, Tanne A, Gruber SB, Johnson TM, Fullen DR, Raskin L, Phelps R, Bhardwaj N, Bernstein E, Ting DT, Brunner G, Schadt EE, Greenbaum BD, Celebi JT. Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation. JCI Insight 2017; 2:92102. [PMID: 28469092 PMCID: PMC5414564 DOI: 10.1172/jci.insight.92102] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/07/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Melanoma is a heterogeneous malignancy. We set out to identify the molecular underpinnings of high-risk melanomas, those that are likely to progress rapidly, metastasize, and result in poor outcomes. METHODS We examined transcriptome changes from benign states to early-, intermediate-, and late-stage tumors using a set of 78 treatment-naive melanocytic tumors consisting of primary melanomas of the skin and benign melanocytic lesions. We utilized a next-generation sequencing platform that enabled a comprehensive analysis of protein-coding and -noncoding RNA transcripts. RESULTS Gene expression changes unequivocally discriminated between benign and malignant states, and a dual epigenetic and immune signature emerged defining this transition. To our knowledge, we discovered previously unrecognized melanoma subtypes. A high-risk primary melanoma subset was distinguished by a 122-epigenetic gene signature ("epigenetic" cluster) and TP53 family gene deregulation (TP53, TP63, and TP73). This subtype associated with poor overall survival and showed enrichment of cell cycle genes. Noncoding repetitive element transcripts (LINEs, SINEs, and ERVs) that can result in immunostimulatory signals recapitulating a state of "viral mimicry" were significantly repressed. The high-risk subtype and its poor predictive characteristics were validated in several independent cohorts. Additionally, primary melanomas distinguished by specific immune signatures ("immune" clusters) were identified. CONCLUSION The TP53 family of genes and genes regulating the epigenetic machinery demonstrate strong prognostic and biological relevance during progression of early disease. Gene expression profiling of protein-coding and -noncoding RNA transcripts may be a better predictor for disease course in melanoma. This study outlines the transcriptional interplay of the cancer cell's epigenome with the immune milieu with potential for future therapeutic targeting. FUNDING National Institutes of Health (CA154683, CA158557, CA177940, CA087497-13), Tisch Cancer Institute, Melanoma Research Foundation, the Dow Family Charitable Foundation, and the Icahn School of Medicine at Mount Sinai.
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Affiliation(s)
- Brateil Badal
- Department of Pathology
- Department of Dermatology
- Department of Oncological Sciences, and
| | - Alexander Solovyov
- Department of Pathology
- Department of Oncological Sciences, and
- Department of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Serena Di Cecilia
- Department of Pathology
- Department of Dermatology
- Department of Oncological Sciences, and
| | - Joseph Minhow Chan
- Department of Pathology
- Department of Dermatology
- Department of Oncological Sciences, and
| | - Li-Wei Chang
- Department of Pathology
- Department of Dermatology
- Department of Oncological Sciences, and
| | - Ramiz Iqbal
- Department of Pathology
- Department of Dermatology
- Department of Oncological Sciences, and
| | - Iraz T. Aydin
- Department of Pathology
- Department of Dermatology
- Department of Oncological Sciences, and
| | - Geena S. Rajan
- Department of Pathology
- Department of Dermatology
- Department of Oncological Sciences, and
| | | | - Franco Abbate
- Department of Pathology
- Department of Dermatology
- Department of Oncological Sciences, and
| | - Kshitij S. Arora
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Antoine Tanne
- Department of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen B. Gruber
- Department of Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | | | - Douglas R. Fullen
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Leon Raskin
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Nina Bhardwaj
- Department of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emily Bernstein
- Department of Dermatology
- Department of Oncological Sciences, and
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David T. Ting
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Georg Brunner
- Department of Cancer Research, Fachklinik Hornheide, Munster, Germany
| | - Eric E. Schadt
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin D. Greenbaum
- Department of Pathology
- Department of Oncological Sciences, and
- Department of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Julide Tok Celebi
- Department of Pathology
- Department of Dermatology
- Department of Oncological Sciences, and
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Puig-Butille JA, Gimenez-Xavier P, Visconti A, Nsengimana J, Garcia-García F, Tell-Marti G, Escamez MJ, Newton-Bishop J, Bataille V, del Río M, Dopazo J, Falchi M, Puig S. Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis. Oncotarget 2017; 8:11589-11599. [PMID: 28030792 PMCID: PMC5355288 DOI: 10.18632/oncotarget.14140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/21/2016] [Indexed: 12/11/2022] Open
Abstract
The MC1R gene plays a crucial role in pigmentation synthesis. Loss-of-function MC1R variants, which impair protein function, are associated with red hair color (RHC) phenotype and increased skin cancer risk. Cultured cutaneous cells bearing loss-of-function MC1R variants show a distinct gene expression profile compared to wild-type MC1R cultured cutaneous cells. We analysed the gene signature associated with RHC co-cultured melanocytes and keratinocytes by Protein-Protein interaction (PPI) network analysis to identify genes related with non-functional MC1R variants. From two detected networks, we selected 23 nodes as hub genes based on topological parameters. Differential expression of hub genes was then evaluated in healthy skin biopsies from RHC and black hair color (BHC) individuals. We also compared gene expression in melanoma tumors from individuals with RHC versus BHC. Gene expression in normal skin from RHC cutaneous cells showed dysregulation in 8 out of 23 hub genes (CLN3, ATG10, WIPI2, SNX2, GABARAPL2, YWHA, PCNA and GBAS). Hub genes did not differ between melanoma tumors in RHC versus BHC individuals. The study suggests that healthy skin cells from RHC individuals present a constitutive genomic deregulation associated with the red hair phenotype and identify novel genes involved in melanocyte biology.
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Affiliation(s)
- Joan Anton Puig-Butille
- Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clinic & IDIBAPS, CIBER de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Pol Gimenez-Xavier
- Dermatology Department, Melanoma Unit, Hospital Clinic & IDIBAPS, CIBER de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Francisco Garcia-García
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Gemma Tell-Marti
- Dermatology Department, Melanoma Unit, Hospital Clinic & IDIBAPS, CIBER de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Maria José Escamez
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, CIEMAT, IIS-Fundación Jiménez Díaz, CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Marcela del Río
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, CIEMAT, IIS-Fundación Jiménez Díaz, CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
- Functional Genomics Node, (INB) at CIPF, Valencia, Spain
- CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clinic & IDIBAPS, CIBER de Enfermedades Raras (CIBERER), Barcelona, Spain
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Zainulabadeen A, Yao P, Zare H. Underexpression of Specific Interferon Genes Is Associated with Poor Prognosis of Melanoma. PLoS One 2017; 12:e0170025. [PMID: 28114321 PMCID: PMC5256985 DOI: 10.1371/journal.pone.0170025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/26/2016] [Indexed: 01/30/2023] Open
Abstract
Because the prognosis of melanoma is challenging and inaccurate when using current clinical approaches, clinicians are seeking more accurate molecular markers to improve risk models. Accordingly, we performed a survival analysis on 404 samples from The Cancer Genome Atlas (TCGA) cohort of skin cutaneous melanoma. Using our recently developed gene network model, we identified biological signatures that confidently predict the prognosis of melanoma (p-value < 10-5). Our model predicted 38 cases as low-risk and 54 cases as high-risk. The probability of surviving at least 5 years was 64% for low-risk and 14% for high-risk cases. In particular, we found that the overexpression of specific genes in the mitotic cell cycle pathway and the underexpression of specific genes in the interferon pathway are both associated with poor prognosis. We show that our predictive model assesses the risk more accurately than the traditional Clark staging method. Therefore, our model can help clinicians design treatment strategies more effectively. Furthermore, our findings shed light on the biology of melanoma and its prognosis. This is the first in vivo study that demonstrates the association between the interferon pathway and the prognosis of melanoma.
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Affiliation(s)
- Aamir Zainulabadeen
- Department of Computer Science, Texas State University, San Marcos, Texas, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| | - Philip Yao
- Department of Computer Science, Texas State University, San Marcos, Texas, United States of America
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Habil Zare
- Department of Computer Science, Texas State University, San Marcos, Texas, United States of America
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Lauss M, Nsengimana J, Staaf J, Newton-Bishop J, Jönsson G. Consensus of Melanoma Gene Expression Subtypes Converges on Biological Entities. J Invest Dermatol 2016; 136:2502-2505. [PMID: 27345472 DOI: 10.1016/j.jid.2016.05.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/09/2016] [Accepted: 05/31/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Martin Lauss
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, Sweden
| | - Jeremie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Johan Staaf
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, Sweden
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Göran Jönsson
- Department of Oncology and Pathology, Clinical Sciences, Lund University Hospital, Lund University, Lund, Sweden.
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O'Shea SJ, Davies JR, Newton-Bishop JA. Vitamin D, vitamin A, the primary melanoma transcriptome and survival. Br J Dermatol 2016; 175 Suppl 2:30-34. [PMID: 27667313 PMCID: PMC5053247 DOI: 10.1111/bjd.14919] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 12/21/2022]
Abstract
Survival from melanoma is influenced by several, well-established clinical and histopathological factors, e.g. age, Breslow thickness and microscopic ulceration. We (the Section of Epidemiology and Biostatistics, University of Leeds) have carried out research to better understand the biological basis for these observations. Preliminary results indicated a protective role for vitamin D in melanoma relapse and that higher vitamin D was associated with thinner primary melanomas. Funding from the British Skin Foundation enabled JNB to establish a study of the effects of vitamin A in melanoma. The results suggested that vitamin A could reduce the protective effect of vitamin D in terms of overall survival. Therefore, we propose that vitamin D3 supplementation alone might be preferable to combined multivitamin preparations, where vitamin D supplementation is deemed to be appropriate. Proving a causal link between vitamin D and melanoma-specific survival is challenging. We have shown limited evidence of causation in a Mendelian randomization experiment (described in more detail later). Recent work in Leeds has also shown that higher vitamin D may be protective for microscopic ulceration. Taken together, vitamin D appears to be associated with less aggressive primary melanomas and may itself influence outcome. We continue to explore the role of vitamin D in melanoma survival and the optimum levels that might be crucial.
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Affiliation(s)
- S J O'Shea
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Genetics Building, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - J R Davies
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Genetics Building, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - J A Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Genetics Building, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK.
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Eriksson H, Lyth J, Andersson TML. The proportion cured of patients diagnosed with Stage III-IV cutaneous malignant melanoma in Sweden 1990-2007: A population-based study. Int J Cancer 2016; 138:2829-36. [PMID: 26815934 DOI: 10.1002/ijc.30023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/30/2015] [Accepted: 01/15/2016] [Indexed: 02/03/2023]
Abstract
The survival in cutaneous malignant melanoma (CMM) is highly dependent on the stage of the disease. Stage III-IV CMM patients are at high risk of relapse with a heterogeneous outcome, but not all experience excess mortality due to their disease. This group is referred to as the cure proportion representing the proportion of patients who experience the same mortality rate as the general population. The aim of this study was to estimate the cure proportion of patients diagnosed with Stage III-IV CMM in Sweden. From the population-based Swedish Melanoma Register, we included 856 patients diagnosed with primary Stage III-IV CMM, 1990-2007, followed-up through 2013. We used flexible parametric cure models to estimate cure proportions and median survival times (MSTs) of uncured by sex, age, tumor site, ulceration status (in Stage III patients) and disease stage. The standardized (over sex, age and site) cure proportion was lower in Stage IV CMMs (0.15, 95% CI 0.09-0.22) than non-ulcerated Stage III CMMs (0.48, 95% CI 0.41-0.55) with a statistically significant difference of 0.33 (95% CI = 0.24-0.41). Ulcerated Stage III CMMs had a cure proportion of 0.27 (95% CI 0.21-0.32) with a statistically significant difference compared to non-ulcerated Stage III CMMs (difference 0.21; 95% CI = 0.13-0.30). The standardized MST of uncured was approximately 9-10 months longer for non-ulcerated versus ulcerated Stage III CMMs. We could demonstrate a significantly better outcome in patients diagnosed with non-ulcerated Stage III CMMs compared to ulcerated Stage III CMMs and Stage IV disease after adjusting for age, sex and tumor site.
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Affiliation(s)
- Hanna Eriksson
- Department of Oncology-Pathology, Karolinska Institutet, and Deptartment of Oncology, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Johan Lyth
- Unit of Research and Development in Local Health Care, County of Östergötland, Linköping, Sweden
| | - Therese M-L Andersson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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