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Dobre EG, Nichita L, Popp C, Zurac S, Neagu M. Assessment of RAS-RAF-MAPK Pathway Mutation Status in Healthy Skin, Benign Nevi, and Cutaneous Melanomas: Pilot Study Using Droplet Digital PCR. Int J Mol Sci 2024; 25:2308. [PMID: 38396984 PMCID: PMC10889428 DOI: 10.3390/ijms25042308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
In the present study, we employed the ddPCR and IHC techniques to assess the prevalence and roles of RAS and RAF mutations in a small batch of melanoma (n = 22), benign moles (n = 15), and normal skin samples (n = 15). Mutational screening revealed the coexistence of BRAF and NRAS mutations in melanomas and nevi and the occurrence of NRAS G12/G13 variants in healthy skin. All investigated nevi had driver mutations in the BRAF or NRAS genes and elevated p16 protein expression, indicating cell cycle arrest despite an increased mutational burden. BRAF V600 mutations were identified in 54% of melanomas, and NRAS G12/G13 mutations in 50%. The BRAF mutations were associated with the Breslow index (BI) (p = 0.029) and TIL infiltration (p = 0.027), whereas the NRAS mutations correlated with the BI (p = 0.01) and the mitotic index (p = 0.04). Here, we demonstrate that the "young" ddPCR technology is as effective as a CE-IVD marked real-time PCR method for detecting BRAF V600 hotspot mutations in tumor biopsies and recommend it for extended use in clinical settings. Moreover, ddPCR was able to detect low-frequency hotspot mutations, such as NRAS G12/G13, in our tissue specimens, which makes it a promising tool for investigating the mutational landscape of sun-damaged skin, benign nevi, and melanomas in more extensive clinical studies.
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Affiliation(s)
- Elena-Georgiana Dobre
- Doctoral School, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
| | - Luciana Nichita
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
- Colentina Clinical Hospital, 020125 Bucharest, Romania
- Department of Pathology, Faculty of Dental Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Cristiana Popp
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
- Colentina Clinical Hospital, 020125 Bucharest, Romania
- Department of Pathology, Faculty of Dental Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Sabina Zurac
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
- Colentina Clinical Hospital, 020125 Bucharest, Romania
- Department of Pathology, Faculty of Dental Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Monica Neagu
- Doctoral School, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
- “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania; (L.N.); (C.P.); (S.Z.)
- Colentina Clinical Hospital, 020125 Bucharest, Romania
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Kerkour T, Zhou C, Hollestein L, Mooyaart A. Genetic Concordance in Primary Cutaneous Melanoma and Matched Metastasis: A Systematic Review and Meta-Analysis. Int J Mol Sci 2023; 24:16281. [PMID: 38003476 PMCID: PMC10671327 DOI: 10.3390/ijms242216281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Studying primary melanoma and its corresponding metastasis has twofold benefits. Firstly, to better understand tumor biology, and secondly, to determine which sample should be examined in assessing drug targets. This study systematically analyzed all the literature on primary melanoma and its matched metastasis. Following PRISMA guidelines, we searched multiple medical databases for relevant publications from January 2000 to December 2022, assessed the quality of the primary-level studies using the QUIPS tool, and summarized the concordance rate of the most reported genes using the random-effects model. Finally, we evaluated the inter-study heterogeneity using the subgroup analysis. Thirty-one studies investigated the concordance of BRAF and NRAS in 1220 and 629 patients, respectively. The pooled concordance rate was 89.4% [95% CI: 84.5; 93.5] for BRAF and 97.8% [95% CI: 95.8; 99.4] for NRAS. When high-quality studies were considered, only BRAF mutation status consistency increased. Five studies reported the concordance status of c-KIT (93%, 44 patients) and TERT promoter (64%, 53 patients). Lastly, three studies analyzed the concordance of cancer genes involved in the signaling pathways, apoptosis, and proliferation, such as CDKN2A (25%, four patients), TP53 (44%, nine patients), and PIK3CA (20%, five patients). Our study found that the concordance of known drug targets (mainly BRAF) during melanoma progression is higher than in previous meta-analyses, likely due to advances in molecular techniques. Furthermore, significant heterogeneity exists in the genes involved in the melanoma genetic makeup; although our results are based on small patient samples, more research is necessary for validation.
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Affiliation(s)
- Thamila Kerkour
- Department of Dermatology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (T.K.); (C.Z.); (L.H.)
| | - Catherine Zhou
- Department of Dermatology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (T.K.); (C.Z.); (L.H.)
| | - Loes Hollestein
- Department of Dermatology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (T.K.); (C.Z.); (L.H.)
| | - Antien Mooyaart
- Department of Pathology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands
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Mandalà M, Palmieri G, Ludovini V, Baglivo S, Marasciulo F, Castiglione F, Gili A, Osella Abate S, Rubatto M, Senetta R, Avallone G, Ribero S, Romano L, Pimpinelli N, de Giorgi V, Roila F, Pisano M, Casula M, Manca A, Sini MC, Massi D, Quaglino P. BRAFV600 variant allele frequency predicts outcome in metastatic melanoma patients treated with BRAF and MEK inhibitors. J Eur Acad Dermatol Venereol 2023; 37:1991-1998. [PMID: 37335879 DOI: 10.1111/jdv.19281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/26/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND The prognostic impact of variant allele frequency (VAF) on clinical outcome in BRAFV600 mutated metastatic melanoma patients (MMPs) receiving BRAF (BRAFi) and MEK inhibitors (MEKi) is unclear. MATERIALS AND METHODS A cohort of MMPs receiving first line BRAFi and MEKi was identified by inspecting dedicated databases of three Italian Melanoma Intergroup centres. VAF was determined by next generation sequencing in pre-treatment baseline tissue samples. Correlation between VAF and BRAF copy number variation was analysed in an ancillary study by using a training and a validation cohort of melanoma tissue samples and cell lines. RESULTS Overall, 107 MMPs were included in the study. The VAF cut-off determined by ROC curve was 41.3%. At multivariate analysis, progression-free survival (PFS) was significantly shorter in patients with M1c/M1d [HR 2.25 (95% CI 1.41-3.6, p < 0.01)], in those with VAF >41.3% [HR 1.62 (95% CI 1.04-2.54, p < 0.05)] and in those with ECOG PS ≥1 [HR 1.82 (95% CI 1.15-2.88, p < 0.05)]. Overall survival (OS) was significantly shorter in patients with M1c/M1d [HR 2.01 (95% CI 1.25-3.25, p < 0.01)]. Furthermore, OS was shorter in patients with VAF >41.3% [HR 1.46 (95% CI 0.93-2.29, p = 0.06)] and in patients with ECOG PS ≥1 [HR 1.52 (95% CI 0.94-2.87, p = 0.14)]. BRAF gene amplification was found in 11% and 7% of samples in the training and validation cohort, respectively. CONCLUSIONS High VAF is an independent poor prognostic factor in MMP receiving BRAFi and MEKi. High VAF and BRAF amplification coexist in 7%-11% of patients.
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Affiliation(s)
- Mario Mandalà
- University of Perugia, Perugia, Italy
- Unit of Medical Oncology, Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Giuseppe Palmieri
- Immuno-Oncology & Targeted Cancer Biotherapies, University of Sassari, Sassari, Italy
- Unit of Cancer Genetics, IRGB-CNR, Sassari, Italy
| | - Vienna Ludovini
- Unit of Medical Oncology, Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Sara Baglivo
- Unit of Medical Oncology, Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Francesca Marasciulo
- Unit of Medical Oncology, Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Francesca Castiglione
- Histopathology and Molecular Diagnostics, Careggi University Hospital, Florence, Italy
| | - Alessio Gili
- Unit of Medical Oncology, Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Simona Osella Abate
- Pathology Unit, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Marco Rubatto
- Dermatology Unit, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Rebecca Senetta
- Pathology Division, "Città della Salute e della Scienza di Torino" University Hospital, Torino, Italy
| | - Gianluca Avallone
- Dermatology Unit, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Simone Ribero
- Dermatology Unit, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Luca Romano
- Unit of Medical Oncology, Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Nicola Pimpinelli
- Unit of Dermatology, Department of Health Sciences, University of Florence Medical School, Florence, Italy
| | - Vincenzo de Giorgi
- Unit of Dermatology, Department of Health Sciences, University of Florence Medical School, Florence, Italy
| | - Fausto Roila
- University of Perugia, Perugia, Italy
- Unit of Medical Oncology, Santa Maria della Misericordia Hospital, Perugia, Italy
| | | | | | | | | | - Daniela Massi
- Section of Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Pietro Quaglino
- Dermatology Unit, Department of Medical Sciences, University of Torino, Torino, Italy
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Stark MS, Harris T, Grossman D, Judson-Torres R. BRAF variant allele fraction-A predictor of response to targeted therapy? J Eur Acad Dermatol Venereol 2023; 37:1945-1946. [PMID: 37746754 DOI: 10.1111/jdv.19389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 07/31/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Mitchell S Stark
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Teresa Harris
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Douglas Grossman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, Utah, USA
- Department of Dermatology, School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Robert Judson-Torres
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, Utah, USA
- Department of Dermatology, School of Medicine, University of Utah, Salt Lake City, Utah, USA
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Tachibana K, Goto K, Kukita Y, Honma K, Isei T, Sugihara S, Taniguchi K, Yamasaki O. BRAF Immunoexpression Can Be Intralesionally Heterogeneous but BRAF V600E Mutation Status Is Intralesionally Homogeneous and Interlesionally Concordant in Melanoma: A Study of 140 Lesions From 98 Patients. Am J Dermatopathol 2022; 44:478-487. [PMID: 35120030 DOI: 10.1097/dad.0000000000002146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
ABSTRACT This study sought to confirm the homogeneity of BRAF V600E mutation status in melanoma. BRAF immunohistochemistry was performed on 102 lesions from 60 patients of melanoma with BRAF V600E mutation and 38 negative-control melanoma lesions from 38 patients, both of which were confirmed by real-time PCR or the MassARRAY System. In the positive-control lesions, 9 lesions from 7 patients with preceding BRAF-inhibitor therapy were included. Of the 102 BRAF-mutant lesions, 101 (99.0%) showed diffuse BRAF immunoexpression, but 39 (38.2%) of them showed various heterogeneous intensities. The heterogeneous intensity of immunostaining was due to necrosis (n = 10), minimal or clear cytoplasm (n = 5), tissue crush (n = 8), insufficient fixation (n = 24), or technical error (n = 4). Only 1 lesion (1.0%) with nondiffuse immunoexpression harbored 80% weakly BRAF-positive tumor area and 20% BRAF-negative area with tissue damage. Sanger sequencing performed on the weak or negative regions in 7 lesions revealed BRAF V600E mutation in all the tested lesions. By contrast, all 38 negative-control lesions demonstrated no BRAF immunoexpression. This study demonstrated intralesional homogeneity and interlesional concordance for BRAF V600E mutation status and intralesional frequent heterogeneity for BRAF immunoexpression. The abovementioned 5 phenomena caused substantial reduction in BRAF immunostaining intensity. In 9 lesions within this study, BRAF immunoexpression and BRAF V600E point mutation status were not affected by preceding BRAF inhibitor therapy. Our data would also support the position that it does not matter whether we select primary or metastatic samples for BRAF mutation analysis.
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Affiliation(s)
- Kota Tachibana
- Department of Dermatologic Oncology, Osaka International Cancer Institute, Osaka, Japan
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
- Department of Dermatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Melanoma Center, Okayama University Hospital, Okayama, Japan
| | - Keisuke Goto
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital, Tokyo, Japan
- Department of Pathology, Itabashi Central Clinical Laboratory, Tokyo, Japan
- Department of Anatomic Pathology, Tokyo Medical University, Tokyo, Japan
- Department of Diagnostic Pathology, Shizuoka Cancer Center Hospital, Sunto, Japan
- Department of Clinical Laboratory and Diagnostic Pathology, Osaka National Hospital, Osaka, Japan
- Department of Dermatology, Hyogo Cancer Center, Akashi, Japan
| | - Yoji Kukita
- Laboratory of Genomic Pathology, Research Center, Osaka International Cancer Institute, Osaka, Japan; and
| | - Keiichiro Honma
- Department of Diagnostic Pathology and Cytology, Osaka International Cancer Institute, Osaka, Japan
| | - Taiki Isei
- Department of Dermatologic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Satoru Sugihara
- Department of Dermatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Melanoma Center, Okayama University Hospital, Okayama, Japan
| | - Kohei Taniguchi
- Department of Pathology, Okayama University Hospital, Okayama, Japan
| | - Osamu Yamasaki
- Department of Dermatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Melanoma Center, Okayama University Hospital, Okayama, Japan
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Long-mira E, Picard-gauci A, Lassalle S, Hofman V, Lalvée S, Tanga V, Zahaf K, Bonnetaud C, Lespinet V, Camuzard O, Montaudié H, Poissonnet G, Passeron T, Ilié M, Hofman P. Comparison of Two Rapid Assays for the Detection of BRAF V600 Mutations in Metastatic Melanoma including Positive Sentinel Lymph Nodes. Diagnostics (Basel) 2022; 12:751. [PMID: 35328303 PMCID: PMC8947166 DOI: 10.3390/diagnostics12030751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/01/2023] Open
Abstract
Testing for the BRAF mutation is mandatory for the management of patients with locally advanced or metastatic melanoma. Molecular analysis based on DNA sequencing remains the gold-standard method for the screening of the different BRAF mutations. These methods must be rapid, sensitive, and specific enough to allow optimal therapeutic management in daily practice and also to include patients in clinical trials. Here, we compared the Idylla BRAF Mutation Test and the anti-BRAF V600E (clone VE1) immunohistochemistry (IHC) in 90 melanoma samples, with a focus on a challenging cohort of 32 positive sentinel lymph nodes. The BRAF status was assessed with both methods independently of the percentage of tumor cells. The concordance rate was calculated excluding both non-contributory analyses and BRAFV600K/R/M mutants due to the specific V600E-IHC test design. The incidence of the BRAFV600E mutation was 33% with both BRAF Idylla and BRAF IHC. The agreement rate was 91% (72/79). Although the agreement rate was high, we suggest that the use of IHC is more suitable for rapid BRAF testing on sentinel lymph node biopsies when associated with a low percentage and scattered tumor cells, which gave a high risk of non-contributory analysis and/or false negative results with the IdyllaTMBRAF Mutation Test.
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Falkenius J, Keskitalo J, Kanter L, Johansson H, Höiom V, Hansson J, Egyhazi Brage S. A biomarker panel predicts recurrence-free survival in ulcerated primary cutaneous melanoma. Acta Oncol 2022; 61:14-21. [PMID: 34694198 DOI: 10.1080/0284186x.2021.1989719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Ulceration is an independent adverse prognostic factor in cutaneous malignant melanoma (CMM). There is, however, a need for additional prognostic markers to identify patients with ulcerated stage I-II CMM who have a high-risk for recurrence. The aim of this study was to examine the prognostic impact of BRAF mutation, proliferation and presence of tumour infiltrating lymphocytes (TILs) in primary ulcerated CMM. MATERIAL AND METHODS We have used a consecutive cohort consisting of 71 primary ulcerated CMM (T1b-T4b). BRAF mutation was detected using Cobas test and pyrosequencing. Protein expression of the proliferation marker Ki67 was analysed using immunohistochemistry. Presence of TILs was evaluated in representative hematoxylin-eosin stained formalin-fixed paraffin-embedded tumour sections. RESULTS Proportion of BRAF mutated alleles, proliferation and presence of TILs all had a statistically significant impact on recurrence free survival in univariate analyses (HR 2.44, 95% CI 1.23-4.84, p = 0.011; HR 2.66, 95% CI 1.32-5.35, p = 0.006 respectively HR 0.48, 95% CI 0.24-0.98, p = 0.045). A trend test found a statistically significant decrease in the proportion of recurrence by including the three favourable factors (BRAF wildtype/low proportion of BRAF mutated alleles, low proliferation and high presence of TILs) (p = 0.0004). When at least two out of three factors were present there was a statistically significant association with longer recurrence free survival in the multivariate analysis (HR 0.30, 95% CI 0.15-0.61, p = 0.001) when adjusted for Breslow thickness, an established independent prognostic marker for CMM. CONCLUSION Thus, this panel of markers could be an interesting novel concept for predicting the clinical outcome in patients with high-risk stage I-II ulcerated CMM.
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Affiliation(s)
- Johan Falkenius
- Department of Oncology-Pathology, Karolinska Institutet, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Keskitalo
- Department of Oncology-Pathology, Karolinska Institutet, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Lena Kanter
- Department of Oncology-Pathology, Karolinska Institutet, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Hemming Johansson
- Department of Oncology-Pathology, Karolinska Institutet, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Veronica Höiom
- Department of Oncology-Pathology, Karolinska Institutet, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Suzanne Egyhazi Brage
- Department of Oncology-Pathology, Karolinska Institutet, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
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Soria X, Vilardell F, Maiques Ó, Barceló C, Sisó P, de la Rosa I, Velasco A, Cuevas D, Santacana M, Gatius S, Matías-Guiu X, Rodrigo A, Macià A, Martí RM. BRAFV600E Mutant Allele Frequency (MAF) Influences Melanoma Clinicopathologic Characteristics. Cancers (Basel) 2021; 13:5073. [PMID: 34680222 PMCID: PMC8533792 DOI: 10.3390/cancers13205073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cutaneous melanoma shows high variability regarding clinicopathological presentation, evolution and prognosis. METHODS Next generation sequencing was performed to analyze hotspot mutations in different areas of primary melanomas (MMp) and their paired metastases. Clinicopathological features were evaluated depending on the degree of variation of the BRAFV600E mutant allele frequency (MAF) in MMp. RESULTS In our cohort of 14 superficial spreading, 10 nodular melanomas and 52 metastases, 17/24 (71%) melanomas had a BRAFV600E mutation and 5/24 (21%) had a NRASQ61 mutation. We observed a high variation of BRAFV600E MAF (H-BRAFV600E) in 7/17 (41%) MMp. The H-BRAFV600E MMp were all located on the trunk, had lower Breslow and mitotic indexes and predominantly, a first nodal metastasis. Regions with spindled tumor cells (Spin) and high lymphocytic infiltrate (HInf) were more frequent in the H-BRAFV600E patients (4/7; 57%), whereas regions with epithelial tumor cells (Epit) and low lymphocytic infiltrate (LInf) were predominant (6/10; 60%) and exclusive in the low BRAFV600E MAF variation tumors (L-BRAFV600E). The H-BRAFV600E/Spin/HInf MMp patients had better prognostic features and nodal first metastasis. CONCLUSIONS The H-BRAFV600E MMp were located on the trunk, had better prognostic characteristics, such as lower Breslow and mitotic indexes as well as high lymphocytic infiltrate.
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Affiliation(s)
- Xavier Soria
- Department of Dermatology, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain;
| | - Felip Vilardell
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
| | - Óscar Maiques
- Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK;
| | - Carla Barceló
- Oncological Pathology Group, Institut de Recerca Biomèdica de Lleida (IRBLleida), 25198 Lleida, Spain; (C.B.); (P.S.); (I.d.l.R.)
| | - Pol Sisó
- Oncological Pathology Group, Institut de Recerca Biomèdica de Lleida (IRBLleida), 25198 Lleida, Spain; (C.B.); (P.S.); (I.d.l.R.)
| | - Inés de la Rosa
- Oncological Pathology Group, Institut de Recerca Biomèdica de Lleida (IRBLleida), 25198 Lleida, Spain; (C.B.); (P.S.); (I.d.l.R.)
| | - Ana Velasco
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Dolors Cuevas
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Maria Santacana
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Sònia Gatius
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Xavier Matías-Guiu
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Alberto Rodrigo
- Department of Medical Oncology, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain;
| | - Anna Macià
- Unitat de Farmacologia- Department of Experimental Medicine, Universitat de Lleida, 25198 Lleida, Spain;
| | - Rosa M. Martí
- Department of Dermatology, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain;
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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9
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Diossy M, Sztupinszki Z, Krzystanek M, Borcsok J, Eklund AC, Csabai I, Pedersen AG, Szallasi Z. Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts. Brief Bioinform 2021; 22:6278604. [PMID: 34015811 DOI: 10.1093/bib/bbab186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/11/2021] [Accepted: 04/22/2021] [Indexed: 12/20/2022] Open
Abstract
Formalin-fixed paraffin-embedded tissue, the most common tissue specimen stored in clinical practice, presents challenges in the analysis due to formalin-induced artifacts. Here, we present Strand Orientation Bias Detector (SOBDetector), a flexible computational platform compatible with all the common somatic SNV-calling pipelines, designed to assess the probability whether a given detected mutation is an artifact. The underlying predictor mechanism is based on the posterior distribution of a Bayesian logistic regression model trained on The Cancer Genome Atlas whole exomes. SOBDetector is a freely available cross-platform program, implemented in Java 1.8.
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Affiliation(s)
| | | | | | - Judit Borcsok
- University of Copenhagen and at the Danish Cancer Society, Copenhagen, Denmark
| | | | - István Csabai
- Department of Complex Physics, Eotvos Lorand University, Budapest, Hungary
| | | | - Zoltan Szallasi
- Boston Children's Hospital and Harvard Medical School, Boston, USA
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10
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Berrino E, Balsamo A, Pisacane A, Gallo S, Becco P, Miglio U, Caravelli D, Poletto S, Paruzzo L, Debernardi C, Piccinelli C, Zaccagna A, Rescigno P, Aglietta M, Sapino A, Carnevale-Schianca F, Venesio T. High BRAF variant allele frequencies are associated with distinct pathological features and responsiveness to target therapy in melanoma patients. ESMO Open 2021; 6:100133. [PMID: 33984673 PMCID: PMC8134716 DOI: 10.1016/j.esmoop.2021.100133] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/02/2021] [Accepted: 04/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background BRAF mutant melanoma patients are commonly treated with anti-BRAF therapeutic strategies. However, many factors, including the percentage of BRAF-mutated cells, may contribute to the great variability in patient outcomes. Patients and methods The BRAF variant allele frequency (VAF; defined as the percentage of mutated alleles) of primary and secondary melanoma lesions, obtained from 327 patients with different disease stages, was assessed by pyrosequencing. The BRAF mutation rate and VAF were then correlated with melanoma pathological features and patients’ clinical characteristics. Kaplan–Meier curves were used to study the correlations between BRAF VAF, overall survival (OS), and progression-free survival (PFS) in a subset of 62 patients treated by anti-BRAF/anti-MEK therapy after metastatic progression. Results A highly heterogeneous BRAF VAF was identified (3%-90%). Besides being correlated with age, a higher BRAF VAF level was related to moderate lymphocytic infiltration (P = 0.017), to melanoma thickness according to Clark levels, (level V versus III, P = 0.004; level V versus IV, P = 0.04), to lymph node metastases rather than cutaneous (P = 0.04) or visceral (P = 0.03) secondary lesions. In particular, a BRAF VAF >25% was significantly associated with a favorable outcome in patients treated with the combination of anti-BRAF/anti-MEK drug (OS P = 0.04; PFS P = 0.019), retaining a significant value as an independent factor for the OS and the PFS in the multivariate analysis (P = 0.014 and P = 0.003, respectively). Conclusion These results definitively support the role of the BRAF VAF as a potential prognostic and predictive biomarker in melanoma patients in the context of BRAF inhibition. In melanoma the response to anti-BRAF targeted therapies is heterogeneous and influenced by several features. The role of the BRAF VAF as provider of sensitivity to target therapies is debated. We found that high BRAF VAFs are associated with patient age, melanoma thickness, non-brisk TILs and lymph node metastases. We proved the independent prognostic value of high BRAF VAFs in melanoma patients treated with targeted therapies. The quantitative evaluation of BRAF mutations allows stratifying melanoma patients to the BRAF/MEK targeted treatment.
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Affiliation(s)
- E Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy
| | - A Balsamo
- Clinical Research Office, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - A Pisacane
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - S Gallo
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - P Becco
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - U Miglio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - D Caravelli
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - S Poletto
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Oncology, University of Turin, Turin, Italy
| | - L Paruzzo
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Oncology, University of Turin, Turin, Italy
| | - C Debernardi
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - C Piccinelli
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - A Zaccagna
- Dermosurgery, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - P Rescigno
- Interdisciplinary Group for Research and Clinical Trials, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy
| | - M Aglietta
- Medical Oncology Division, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Oncology, University of Turin, Turin, Italy
| | - A Sapino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy; Department of Medical Sciences, University of Turin, Turin, Italy.
| | | | - T Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCs, Turin, Italy.
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11
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Abstract
OPINION STATEMENT In the era of molecular targeted therapy, the accurate detection of BRAF mutation in melanoma has become increasingly important. With the advances of molecular analyses and immunohistochemistry, the presence of BRAF mutational heterogeneity in melanoma has been widely recognized. Although most patients with melanoma have a homogeneous BRAF mutation status because the BRAF mutation occurs at an early stage of melanoma development and acts as a driver gene mutation, BRAF mutational heterogeneity does exist, among different tumor sites of a single patient (intertumor heterogeneity) and/or even within a single tumor (intratumor heterogeneity). To summarize the published reports, about 10% of melanoma patients may show intertumorally discordant BRAF status and about 15% of BRAF-mutated melanomas may have intratumor BRAF heterogeneity, although the reported results vary strikingly among the studies and methods used. Considering the BRAF heterogeneity of melanoma, a single biopsy from a single tumor may not be sufficient to uncover the entire BRAF status of a patient. Multiple samples from different sites may be preferable to assess the indication of BRAF/MEK inhibitors, as recommended by the current clinical guidelines. The impact of BRAF heterogeneity on patient survival or the response to treatment with BRAF/MEK inhibitors is an interesting issue, but requires further investigation.
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Affiliation(s)
- Takamichi Ito
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashiku, Fukuoka, 812-8582, Japan.
| | - Yuka Tanaka
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashiku, Fukuoka, 812-8582, Japan
| | - Maho Murata
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashiku, Fukuoka, 812-8582, Japan
| | - Yumiko Kaku-Ito
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashiku, Fukuoka, 812-8582, Japan
| | - Kazuhisa Furue
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashiku, Fukuoka, 812-8582, Japan
| | - Masutaka Furue
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashiku, Fukuoka, 812-8582, Japan
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12
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Yokomichi H, Inozume T, Wada M, Asai J, Igaki H, Namikawa K, Hayashi A, Fukushima S, Fujimura T, Koga H, Nakamura Y, Mochizuki M, Yamagata Z. Concordance and Discordance Rates of V-Raf Murine Sarcoma Viral Oncogene Homolog B1 ( BRAF) V600E Status in Metastatic against Primary Lesion of Melanoma: A Meta-analysis. JMA J 2020; 3:274-279. [PMID: 33150263 PMCID: PMC7590371 DOI: 10.31662/jmaj.2020-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/01/2020] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Takashi Inozume
- Department of Dermatology, University of Yamanashi, Chuo, Japan
| | - Makoto Wada
- Department of Dermatology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Jun Asai
- Department of Dermatology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroshi Igaki
- Department of Radiation Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kenjiro Namikawa
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Ayato Hayashi
- Department of Plastic and Reconstructive Surgery, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - Satoshi Fukushima
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Taku Fujimura
- Department of Dermatology, Tohoku University, Sendai, Japan
| | - Hiroshi Koga
- Department of Dermatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yasuhiro Nakamura
- Department of Skin Oncology/Dermatology, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Mie Mochizuki
- Department of Pediatrics, University of Yamanashi, Chuo, Japan
| | - Zentaro Yamagata
- Department of Health Sciences, University of Yamanashi, Chuo, Japan
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13
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Mejbel HA, Arudra SKC, Pradhan D, Torres-Cabala CA, Nagarajan P, Tetzlaff MT, Curry JL, Ivan D, Duose DY, Luthra R, Prieto VG, Ballester LY, Aung PP. Immunohistochemical and Molecular Features of Melanomas Exhibiting Intratumor and Intertumor Histomorphologic Heterogeneity. Cancers (Basel) 2019; 11:E1714. [PMID: 31684113 PMCID: PMC6896082 DOI: 10.3390/cancers11111714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Melanoma is a heterogeneous neoplasm at the histomorphologic, immunophenotypic, and molecular levels. Melanoma with extreme histomorphologic heterogeneity can pose a diagnostic challenge in which the diagnosis may predominantly rely on its immunophenotypic profile. However, tumor survival and response to therapy are linked to tumor genetic heterogeneity rather than tumor morphology. Therefore, understating the molecular characteristics of such melanomas become indispensable. In this study, DNA was extracted from 11 morphologically distinct regions in eight formalin-fixed, paraffin-embedded melanomas. In each region, mutations in 50 cancer-related genes were tested using next-generation sequencing (NGS). A tumor was considered genetically heterogeneous if at least one non-overlapping mutation was identified either between the histologically distinct regions of the same tumor (intratumor heterogeneity) or among the histologically distinct regions of the paired primary and metastatic tumors within the same patient (intertumor heterogeneity). Our results revealed that genetic heterogeneity existed in all tumors as non-overlapping mutations were detected in every tested tumor (n = 5, 100%; intratumor: n = 2, 40%; intertumor: n = 3, 60%). Conversely, overlapping mutations were also detected in all the tested regions (n = 11, 100%). Melanomas exhibiting histomorphologic heterogeneity are often associated with genetic heterogeneity, which might contribute to tumor survival and poor response to therapy.
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Affiliation(s)
- Haider A Mejbel
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Sri Krishna C Arudra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Dinesh Pradhan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Carlos A Torres-Cabala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Priyadharsini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Jonathan L Curry
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Doina Ivan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Raja Luthra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Victor G Prieto
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Leomar Y Ballester
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Phyu P Aung
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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14
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Doma V, Kárpáti S, Rásó E, Barbai T, Tímár J. Dynamic and unpredictable changes in mutant allele fractions of BRAF and NRAS during visceral progression of cutaneous malignant melanoma. BMC Cancer 2019; 19:786. [PMID: 31391014 PMCID: PMC6686548 DOI: 10.1186/s12885-019-5990-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
Background Data indicate that primary cutaneous melanomas are characterized by clonal heterogeneity associated with oncogenic drivers. Less data are available on the clonal changes occurring during melanoma progression. We therefore wished to analyse these changes in skin melanomas in common sites of visceral metastases as compared to the primary tumor. Methods An autopsy cohort of 50 patients with BRAF- and NRAS-mutant cutaneous metastatic melanomas including 139 visceral metastases was analysed for mutant allele fractions (MAF), determined by pyrosequencing and corrected for tumor/normal ratio. MAF levels were also classified as high (> 40%), medium (15–40%) or low (< 15%). Results Contrary to NRAS mutant cases, in BRAF-mutant melanomas MAFs were found to be significantly increased in visceral metastases compared to the primary due to the significantly higher levels in lung-, adrenal gland-, intestinal- and kidney metastases. The incidence of the three MAF variants in BRAF-mutant primaries was similar, whereas the high MAF cases were found to be increased in metastases. On the other hand, medium MAF levels were more common in case of NRAS-mutant tumors. Only 31.3% of BRAF mutant- and 50% of NRAS mutant cases maintained the MAF profile of the primary in metastasis. In the majority of multiple metastatic tumors, (BRAF:71.8%, NRAS:75%) metastases were relatively homogeneous regarding MAF. However, in 6/32(18.7%) of BRAF mutant cases low MAF primaries switched to high MAF in metastases. In heterogeneous BRAF mutant metastatic cases low to high or high to low MAF conversions occurred in a further 4/32(12.5%) cases in individual metastases as compared to the primary tumors. At lower frequency, in NRAS mutant tumor such changes also observed (2/12,16.7%). Conclusion We provided evidence for the selection of BRAF-mutant melanoma cells during metastatic progression to the lung, intestine, adrenal gland and kidney. Our findings suggest that in visceral metastases of malignant melanoma BRAF- or NRAS-MAFs are rather heterogeneous and cannot be predicted from data of the primary tumor. These data may have clinical significance when using targeted therapies. Electronic supplementary material The online version of this article (10.1186/s12885-019-5990-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V Doma
- 2nd Department of Pathology, Semmelweis University, 93. Üllői, Budapest, H-1091, Hungary.,Department of Dermatology, Semmelweis University, Budapest, Hungary
| | - S Kárpáti
- Department of Dermatology, Semmelweis University, Budapest, Hungary
| | - E Rásó
- 2nd Department of Pathology, Semmelweis University, 93. Üllői, Budapest, H-1091, Hungary
| | - T Barbai
- 2nd Department of Pathology, Semmelweis University, 93. Üllői, Budapest, H-1091, Hungary
| | - J Tímár
- 2nd Department of Pathology, Semmelweis University, 93. Üllői, Budapest, H-1091, Hungary.
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15
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Stagni C, Zamuner C, Elefanti L, Zanin T, Bianco PD, Sommariva A, Fabozzi A, Pigozzo J, Mocellin S, Montesco MC, Chiarion-Sileni V, De Nicolo A, Menin C. BRAF Gene Copy Number and Mutant Allele Frequency Correlate with Time to Progression in Metastatic Melanoma Patients Treated with MAPK Inhibitors. Mol Cancer Ther 2018; 17:1332-1340. [PMID: 29626128 DOI: 10.1158/1535-7163.mct-17-1124] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/07/2018] [Accepted: 03/27/2018] [Indexed: 11/16/2022]
Abstract
Metastatic melanoma is characterized by complex genomic alterations, including a high rate of mutations in driver genes and widespread deletions and amplifications encompassing various chromosome regions. Among them, chromosome 7 is frequently gained in BRAF-mutant melanoma, inducing a mutant allele-specific imbalance. Although BRAF amplification is a known mechanism of acquired resistance to therapy with MAPK inhibitors, it is still unclear if BRAF copy-number variation and BRAF mutant allele imbalance at baseline can be associated with response to treatment. In this study, we used a multimodal approach to assess BRAF copy number and mutant allele frequency in pretreatment melanoma samples from 46 patients who received MAPK inhibitor-based therapy, and we analyzed the association with progression-free survival. We found that 65% patients displayed BRAF gains, often supported by chromosome 7 polysomy. In addition, we observed that 64% patients had a balanced BRAF-mutant/wild-type allele ratio, whereas 14% and 23% patients had low and high BRAF mutant allele frequency, respectively. Notably, a significantly higher risk of progression was observed in patients with a diploid BRAF status versus those with BRAF gains [HR, 2.86; 95% confidence interval (CI), 1.29-6.35; P = 0.01] and in patients with low percentage versus those with a balanced BRAF mutant allele percentage (HR, 4.54; 95% CI, 1.33-15.53; P = 0.016). Our data suggest that quantitative analysis of the BRAF gene could be useful to select the melanoma patients who are most likely to benefit from therapy with MAPK inhibitors. Mol Cancer Ther; 17(6); 1332-40. ©2018 AACR.
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Affiliation(s)
- Camilla Stagni
- Oncology and Immunology Section, Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Carolina Zamuner
- Anatomy and Histology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Lisa Elefanti
- Diagnostic Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Tiziana Zanin
- Anatomy and Histology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Paola Del Bianco
- Clinical Trials and Biostatistics Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Antonio Sommariva
- Surgical Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Alessio Fabozzi
- Melanoma and Esophagus Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Jacopo Pigozzo
- Melanoma and Esophagus Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Simone Mocellin
- Surgical Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | | | - Vanna Chiarion-Sileni
- Melanoma and Esophagus Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Arcangela De Nicolo
- Cancer Genomics Program, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Chiara Menin
- Diagnostic Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, Italy.
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16
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Adler NR, McLean CA, Wolfe R, Kelly JW, McArthur GA, Haydon A, Tra T, Cummings N, Mar VJ. Concordance of somatic mutational profile in multiple primary melanomas. Pigment Cell Melanoma Res 2018; 31:592-603. [PMID: 29603877 DOI: 10.1111/pcmr.12702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/12/2018] [Indexed: 12/16/2022]
Abstract
This study aimed to determine the frequency and concordance of BRAF and NRAS mutation in tumours arising in patients with multiple primary melanoma (MPM). Patients with MPM managed at one of three tertiary referral centres in Melbourne, Australia, from 2010 to 2015 were included. Incident and subsequent melanomas underwent mutation testing. Cohen's kappa (κ) coefficient assessed agreement between incident and subsequent primary melanomas for both BRAF and NRAS mutation status (mutant versus wild-type). Mutation testing of at least two primary tumours from 64 patients was conducted. There was poor agreement for both BRAF and NRAS mutation status between incident and subsequent melanomas (κ = 0.10, 95% CI -0.10 to 0.42; κ = 0.06, 95% CI -0.10 to 0.57, respectively). In view of the low concordance in BRAF mutation status between incident and subsequent melanomas, mutational analysis of metastatic tissue, rather than of a primary melanoma, in patients with MPM should be used to guide targeted therapy.
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Affiliation(s)
- Nikki R Adler
- Victorian Melanoma Service, Alfred Hospital, Melbourne, Vic., Australia.,School of Public Health and Preventive Medicine, Monash University, Melbourne, Vic., Australia
| | - Catriona A McLean
- Victorian Melanoma Service, Alfred Hospital, Melbourne, Vic., Australia.,Department of Anatomical Pathology, Alfred Hospital, Melbourne, Vic., Australia
| | - Rory Wolfe
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Vic., Australia
| | - John W Kelly
- Victorian Melanoma Service, Alfred Hospital, Melbourne, Vic., Australia
| | - Grant A McArthur
- Divisions of Research and Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic., Australia
| | - Andrew Haydon
- Victorian Melanoma Service, Alfred Hospital, Melbourne, Vic., Australia.,Department of Medical Oncology, Alfred Hospital, Melbourne, Vic., Australia
| | - Thien Tra
- Department of Anatomical Pathology, Alfred Hospital, Melbourne, Vic., Australia
| | - Nicholas Cummings
- Department of Anatomical Pathology, Alfred Hospital, Melbourne, Vic., Australia
| | - Victoria J Mar
- Victorian Melanoma Service, Alfred Hospital, Melbourne, Vic., Australia.,School of Public Health and Preventive Medicine, Monash University, Melbourne, Vic., Australia.,Skin and Cancer Foundation Inc., Carlton, Vic., Australia
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17
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Grzywa TM, Paskal W, Włodarski PK. Intratumor and Intertumor Heterogeneity in Melanoma. Transl Oncol 2017; 10:956-975. [PMID: 29078205 PMCID: PMC5671412 DOI: 10.1016/j.tranon.2017.09.007] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/14/2017] [Accepted: 09/17/2017] [Indexed: 12/25/2022] Open
Abstract
Melanoma is a cancer that exhibits one of the most aggressive and heterogeneous features. The incidence rate escalates. A high number of clones harboring various mutations contribute to an exceptional level of intratumor heterogeneity of melanoma. It also refers to metastases which may originate from different subclones of primary lesion. Such component of the neoplasm biology is termed intertumor and intratumor heterogeneity. These levels of tumor heterogeneity hinder accurate diagnosis and effective treatment. The increasing number of research on the topic reflects the need for understanding limitation or failure of contemporary therapies. Majority of analyses concentrate on mutations in cancer-related genes. Novel high-throughput techniques reveal even higher degree of variations within a lesion. Consolidation of theories and researches indicates new routes for treatment options such as targets for immunotherapy. The demand for personalized approach in melanoma treatment requires extensive knowledge on intratumor and intertumor heterogeneity on the level of genome, transcriptome/proteome, and epigenome. Thus, achievements in exploration of melanoma variety are described in details. Particularly, the issue of tumor heterogeneity or homogeneity given BRAF mutations is discussed.
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Affiliation(s)
- Tomasz M Grzywa
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1b, 02-091 Warsaw, Poland
| | - Wiktor Paskal
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1b, 02-091 Warsaw, Poland
| | - Paweł K Włodarski
- The Department of Histology and Embryology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, Banacha 1b, 02-091 Warsaw, Poland.
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18
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Kaczorowski M, Borowiec T, Donizy P, Pagacz K, Fendler W, Lipinski A, Halon A, Matkowski R. Polo-like kinase-1 immunoreactivity is associated with metastases in cutaneous melanoma. J Cutan Pathol 2017; 44:819-826. [PMID: 28626898 DOI: 10.1111/cup.12985] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/05/2017] [Accepted: 06/13/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Polo-like kinase-1 (PLK-1) is one of the key regulators of cell cycle progression. Increased expression of PLK-1 was observed in several tumor types. METHODS We immunohistochemically assessed PLK-1 expression in neoplastic and stromal compartments of 96 cutaneous melanomas, and analyzed associations between PLK-1 expression and clinicopathological characteristics. RESULTS PLK-1 expression in cancer cells was not associated with basic clinical (eg, age, gender and tumor location) or histopathological (eg, Breslow thickness, mitotic rate and ulceration) parameters. However, increased PLK-1 was more frequent in tumors with concurrent regional nodal metastases and positive sentinel lymph node biopsy status. All primary tumors associated with co-existing distant metastases exhibited high PLK-1 expression in melanoma cells. Conversely, PLK-1 expression in stromal cells was more frequent in tumors without nodal metastases. PLK-1 expression in both compartments was not associated with survival. CONCLUSION PLK-1 expression is associated with metastatic potential in cutaneous melanoma.
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Affiliation(s)
- Maciej Kaczorowski
- Department of Pathomorphology and Oncological Cytology, Wroclaw Medical University, Wroclaw, Poland
| | - Tomasz Borowiec
- Department of Oncology and Division of Surgical Oncology, Wroclaw Medical University, Wroclaw, Poland
- Lower Silesian Oncology Centre, Wroclaw, Poland
| | - Piotr Donizy
- Department of Pathomorphology and Oncological Cytology, Wroclaw Medical University, Wroclaw, Poland
| | - Konrad Pagacz
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Artur Lipinski
- Department of Pathomorphology and Oncological Cytology, Wroclaw Medical University, Wroclaw, Poland
| | - Agnieszka Halon
- Department of Pathomorphology and Oncological Cytology, Wroclaw Medical University, Wroclaw, Poland
| | - Rafal Matkowski
- Department of Oncology and Division of Surgical Oncology, Wroclaw Medical University, Wroclaw, Poland
- Lower Silesian Oncology Centre, Wroclaw, Poland
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19
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Valachis A, Ullenhag GJ. Discrepancy in BRAF status among patients with metastatic malignant melanoma: A meta-analysis. Eur J Cancer 2017; 81:106-115. [PMID: 28623774 DOI: 10.1016/j.ejca.2017.05.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/01/2017] [Accepted: 05/08/2017] [Indexed: 12/24/2022]
Abstract
The incidence of malignant melanoma is growing rapidly. Approximately half of the cases are BRAF mutated, making treatment with kinase inhibitors a (MEK and BRAF inhibitors) preferred choice in the advanced setting. The vast majority of these patients will benefit from the treatment. It is therefore of vital importance that the BRAF analysis is reliable and reflects the true nature of the tumour. Intraindividual tumour BRAF heterogeneity may exist, and changes of BRAF status over time might occur. We reviewed the literature by searching the PubMed database and 630 potentially relevant studies were identified. Thereafter, studies that investigated intralesional heterogeneity only, studies with ≤10 patients and studies that did not include adequate data to calculate discrepancy rates were excluded. Twenty-two studies met our inclusion criteria and were included in the meta-analysis. The pooled discrepancy rate between primary and metastatic lesions was 13.4% (95% confidence interval [CI]: 9.2-18.2%) while it was 7.3% (95% CI: 3.3-12.6) between two metastatic lesions. The number of patients whose tumoural BRAF status was changed from mutation to wild type and from wild type to mutation, respectively, was comparable. We conclude that a clinically meaningful discrepancy rate in BRAF status both between primary-metastatic and metastatic-metastatic melanoma lesions exists. Our results support the polyclonal model of melanomas in which subclones with different BRAF status co-exist in the same melanoma lesion. In addition, the results indicate a need for biopsy of a metastatic lesion for subsequent BRAF analysis when treatment with kinase inhibitors is considered.
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Affiliation(s)
- Antonis Valachis
- Department of Immunology, Genetics, and Pathology, Uppsala University, Sweden; Centre for Clinical Research Sörmland, Uppsala University, 63188, Eskilstuna, Sweden.
| | - Gustav J Ullenhag
- Department of Immunology, Genetics, and Pathology, Uppsala University, Sweden; Department of Oncology, Uppsala University Hospital, 751 85, Uppsala, Sweden
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20
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Boespflug A, Funck-Brentano E, Hélias-Rodzewicz Z, Maucort-Boulch D, Beauchet A, Bringuier PP, Dumontet C, Emile JF, Saiag P, Dalle S. Reply to "Clinical and therapeutic implications of BRAF mutation heterogeneity in metastatic melanoma" by Mesbah Ardakani et al. Pigment Cell Melanoma Res 2017. [PMID: 28627072 DOI: 10.1111/pcmr.12606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Amélie Boespflug
- Dermatology Unit, Hospices Civils de Lyon, Pierre-Bénite, France.,Cancer Research Center of Lyon, Claude Bernard Lyon-1 University, INSERM1052, CNRS 5286, Lyon, France.,Pathology Department, Hospices Civiles de Lyon, Pierre-Bénite, France
| | - Elisa Funck-Brentano
- Department of Dermatology, Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France.,Research Unit EA 4340 "Biomarkers in cancerology and in hemato-oncology, University of Versailles-Saint-Quentin-en-Yvelines, Université Paris-Saclay, Boulogne-Billancourt, France
| | - Zofia Hélias-Rodzewicz
- Research Unit EA 4340 "Biomarkers in cancerology and in hemato-oncology, University of Versailles-Saint-Quentin-en-Yvelines, Université Paris-Saclay, Boulogne-Billancourt, France
| | - Delphine Maucort-Boulch
- Laboratoire de Biométrie et Biologie Evolutive, Biostatistique-Santé team, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France.,Department of Pathology, Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France
| | - Alain Beauchet
- Department of Public Health, Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France
| | - Pierre-Paul Bringuier
- Medical Oncology Department, Institut de Cancerologie des Hospices Civils de Lyon, Pierre-Bénite, France
| | - Charles Dumontet
- Cancer Research Center of Lyon, Claude Bernard Lyon-1 University, INSERM1052, CNRS 5286, Lyon, France
| | - Jean-François Emile
- Research Unit EA 4340 "Biomarkers in cancerology and in hemato-oncology, University of Versailles-Saint-Quentin-en-Yvelines, Université Paris-Saclay, Boulogne-Billancourt, France.,Laboratoire de Biométrie et Biologie Evolutive, Biostatistique-Santé team, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France.,Department of Pathology, Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France
| | - Philippe Saiag
- Department of Dermatology, Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France.,Research Unit EA 4340 "Biomarkers in cancerology and in hemato-oncology, University of Versailles-Saint-Quentin-en-Yvelines, Université Paris-Saclay, Boulogne-Billancourt, France
| | - Stéphane Dalle
- Dermatology Unit, Hospices Civils de Lyon, Pierre-Bénite, France.,Cancer Research Center of Lyon, Claude Bernard Lyon-1 University, INSERM1052, CNRS 5286, Lyon, France.,Pathology Department, Hospices Civiles de Lyon, Pierre-Bénite, France
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21
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Bruno W, Martinuzzi C, Andreotti V, Pastorino L, Spagnolo F, Dalmasso B, Cabiddu F, Gualco M, Ballestrero A, Bianchi-Scarrà G, Queirolo P, Grillo F, Mastracci L, Ghiorzo P. Heterogeneity and frequency of BRAF mutations in primary melanoma: Comparison between molecular methods and immunohistochemistry. Oncotarget 2017; 8:8069-8082. [PMID: 28039443 PMCID: PMC5352383 DOI: 10.18632/oncotarget.14094] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/24/2016] [Indexed: 11/25/2022] Open
Abstract
Finding the best technique to identify BRAF mutations with a high sensitivity and specificity is mandatory for accurate patient selection for target therapy. BRAF mutation frequency ranges from 40 to 60% depending on melanoma clinical characteristics and detection technique used.Intertumoral heterogeneity could lead to misinterpretation of BRAF mutational status; this is especially important if testing is performed on primary specimens, when metastatic lesions are unavailable.Aim of this study was to identify the best combination of methods for detecting BRAF mutations (among peptide nucleic acid - PNA-clamping real-time PCR, immunohistochemistry and capillary sequencing) and investigate BRAF mutation heterogeneity in a series of 100 primary melanomas and a subset of 25 matched metastatic samples.Overall, we obtained a BRAF mutation frequency of 62%, based on the combination of at least two techniques. Concordance between mutation status in primary and metastatic tumor was good but not complete (67%), when agreement of at least two techniques were considered. Next generation sequencing was used to quantify the threshold of detected mutant alleles in discordant samples. Combining different methods excludes that the observed heterogeneity is technique-based. We propose an algorithm for BRAF mutation testing based on agreement between immunohistochemistry and PNA; a third molecular method could be added in case of discordance of the results. Testing the primary tumor when the metastatic sample is unavailable is a good option if at least two methods of detection are used, however the presence of intertumoral heterogeneity or the occurrence of additional primaries should be carefully considered.
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Affiliation(s)
- William Bruno
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Claudia Martinuzzi
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Virginia Andreotti
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | | | - Bruna Dalmasso
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | | | - Marina Gualco
- Department of Pathology, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Giovanna Bianchi-Scarrà
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Paola Queirolo
- Department of Medical Oncology, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Federica Grillo
- Department of Surgical and Diagnostic Sciences, Pathology Unit, University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Luca Mastracci
- Department of Surgical and Diagnostic Sciences, Pathology Unit, University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa and IRCCS AOU San Martino-IST, Genoa, Italy
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22
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Uguen A, Uguen M. VE1 Immunohistochemistry Fails to Detect Most of the Non-BRAFV600E Mutations in Melanoma. Appl Immunohistochem Mol Morphol 2016; 24:e98-9. [PMID: 26894646 DOI: 10.1097/PAI.0000000000000341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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