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Colombino M, Palmieri G, Rodio M, Tettamanzi M, Rampazzo S, Margani R, Trignano E, Cossu A, Fedeli MA, Fadda GM, Rubino C. Mutational Profiles of Cutaneous Squamous Cell Carcinomas with Different Patterns of Clinical Aggression from Head and Neck Regions. Cancers (Basel) 2024; 16:1956. [PMID: 38893077 PMCID: PMC11171166 DOI: 10.3390/cancers16111956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
Cutaneous squamous cell carcinoma is a prevalent malignancy with a rising incidence and a notably high mutational load. Exploring the genetic nuances of cSCC and investigating molecular approaches stands as a potential avenue for improving outcomes in high-risk patients. This retrospective case-control study involved two cohorts, one of 14 patients (the "discovery cohort") and the other of 12 patients (the "validation cohort"), with cSCC located in the head/neck anatomical region and diagnosed at the pT2 stage. Overall, cases developed early local relapses of the disease, whereas controls never relapsed during the entire follow-up period. A next-generation sequencing (NGS) approach conducted on histological samples revealed that TP53 and CDKN2A were the most frequently mutated genes in our series. No specific mutations were identified as potential prognostic or therapeutic targets. Controls exhibited a tendency toward a higher mutational rate compared to cases. It is possible that an increased number of mutations could prompt the cSCC to expose more antigens, becoming more immunogenic and facilitating recognition by the immune system. This could enhance and sustain the immunological response, potentially preventing future recurrences.
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Affiliation(s)
- Maria Colombino
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), 07100 Sassari, Italy;
| | - Giuseppe Palmieri
- Immuno-Oncology & Targeted Cancer Biotherapies, Unit of Cancer Genetics, Institute of Genetic and Biomolecular Research, National Research Council (CNR), University of Sassari, 07100 Sassari, Italy
| | - Manuela Rodio
- Plastic Surgery Unit, University Hospital Trust of Sassari, 07100 Sassari, Italy; (M.R.); (M.T.); (S.R.); (R.M.); (E.T.); (C.R.)
- Plastic, Reconstructive and Aesthetic Surgery Training Program, University of Sassari, 07100 Sassari, Italy
| | - Matilde Tettamanzi
- Plastic Surgery Unit, University Hospital Trust of Sassari, 07100 Sassari, Italy; (M.R.); (M.T.); (S.R.); (R.M.); (E.T.); (C.R.)
- Plastic, Reconstructive and Aesthetic Surgery Training Program, University of Sassari, 07100 Sassari, Italy
| | - Silvia Rampazzo
- Plastic Surgery Unit, University Hospital Trust of Sassari, 07100 Sassari, Italy; (M.R.); (M.T.); (S.R.); (R.M.); (E.T.); (C.R.)
- Plastic, Reconstructive and Aesthetic Surgery Training Program, University of Sassari, 07100 Sassari, Italy
| | - Raffaello Margani
- Plastic Surgery Unit, University Hospital Trust of Sassari, 07100 Sassari, Italy; (M.R.); (M.T.); (S.R.); (R.M.); (E.T.); (C.R.)
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Emilio Trignano
- Plastic Surgery Unit, University Hospital Trust of Sassari, 07100 Sassari, Italy; (M.R.); (M.T.); (S.R.); (R.M.); (E.T.); (C.R.)
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Antonio Cossu
- Unit of Anatomic Pathology and Histology, University Hospital of Sassari (A.O.U. SS), Via Matteotti 60, 07100 Sassari, Italy; (A.C.); (M.A.F.)
| | - Maria Antonietta Fedeli
- Unit of Anatomic Pathology and Histology, University Hospital of Sassari (A.O.U. SS), Via Matteotti 60, 07100 Sassari, Italy; (A.C.); (M.A.F.)
| | - Giovanni Maria Fadda
- Oncologia Medica, University Hospital of Sassari (A.O.U. SS), 07100 Sassari, Italy;
| | - Corrado Rubino
- Plastic Surgery Unit, University Hospital Trust of Sassari, 07100 Sassari, Italy; (M.R.); (M.T.); (S.R.); (R.M.); (E.T.); (C.R.)
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
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Maloberti T, De Leo A, Coluccelli S, Sanza V, Gruppioni E, Altimari A, Comito F, Melotti B, Marchese PV, Dika E, Venturi F, Corti B, Ciccimarra G, Ciceu CA, Tallini G, de Biase D. Molecular Characterization of Advanced-Stage Melanomas in Clinical Practice Using a Laboratory-Developed Next-Generation Sequencing Panel. Diagnostics (Basel) 2024; 14:800. [PMID: 38667446 PMCID: PMC11048853 DOI: 10.3390/diagnostics14080800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Cutaneous melanoma is one of the most lethal tumors among skin cancers, characterized by complex genetic and molecular alterations that result in uncontrolled cell proliferation and metastatic spread. Next-generation sequencing (NGS) enables the simultaneous examination of numerous genes, making this molecular technique essential for melanoma diagnosis, prognostic stratification, and therapy planning. Herein, we present the experience with our laboratory-designed NGS panel for the routine assessment of advanced-stage melanoma. A total of 260 specimens of advanced-stage melanomas were evaluated utilizing a laboratory-developed multi-gene NGS panel, which allowed the investigation of 229 amplicons in 25 oncogene/oncosuppressor genes. The NGS panel proved to be a reliable tool, failing to produce results in only 1.2% of the samples tested. BRAF and TERT were the two more commonly altered genes in 44.0% and 59.9% of samples, respectively. In 59.3% of the mutated cases, at least two concomitant variants were detected. In eight cases, both primary lesion and metastatic disease were analyzed by NGS. In all specimens (8/8, 100%), a perfect concordance in variants harbored by the primary and recurrence lesions was observed. Finally, this study described the validity of a laboratory-developed multi-gene NGS panel built specifically for advanced-stage melanomas in ordinary clinical practice.
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Affiliation(s)
- Thais Maloberti
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Antonio De Leo
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (E.D.); (F.V.)
| | - Sara Coluccelli
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Viviana Sanza
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Elisa Gruppioni
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Annalisa Altimari
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Francesca Comito
- Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy (B.M.); (P.V.M.)
| | - Barbara Melotti
- Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy (B.M.); (P.V.M.)
| | - Paola Valeria Marchese
- Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy (B.M.); (P.V.M.)
| | - Emi Dika
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (E.D.); (F.V.)
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Federico Venturi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (E.D.); (F.V.)
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Barbara Corti
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Giulia Ciccimarra
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy; (G.C.); (C.A.C.)
| | - Crina Adriana Ciceu
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy; (G.C.); (C.A.C.)
| | - Giovanni Tallini
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (E.D.); (F.V.)
| | - Dario de Biase
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy; (G.C.); (C.A.C.)
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Maher NG, Vergara IA, Long GV, Scolyer RA. Prognostic and predictive biomarkers in melanoma. Pathology 2024; 56:259-273. [PMID: 38245478 DOI: 10.1016/j.pathol.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/20/2023] [Indexed: 01/22/2024]
Abstract
Biomarkers help to inform the clinical management of patients with melanoma. For patients with clinically localised primary melanoma, biomarkers can help to predict post-surgical outcome (including via the use of risk prediction tools), better select patients for sentinel lymph node biopsy, and tailor catch-all follow-up protocols to the individual. Systemic drug treatments, including immune checkpoint inhibitor (ICI) therapies and BRAF-targeted therapies, have radically improved the prognosis of metastatic (stage III and IV) cutaneous melanoma patients, and also shown benefit in the earlier setting of stage IIB/C primary melanoma. Unfortunately, a response is far from guaranteed. Here, we review clinically relevant, established, and emerging, prognostic, and predictive pathological biomarkers that refine clinical decision-making in primary and metastatic melanoma patients. Gene expression profile assays and nomograms are emerging tools for prognostication and sentinel lymph node risk prediction in primary melanoma patients. Biomarkers incorporated into clinical practice guidelines include BRAF V600 mutations for the use of targeted therapies in metastatic cutaneous melanoma, and the HLA-A∗02:01 allele for the use of a bispecific fusion protein in metastatic uveal melanoma. Several predictive biomarkers have been proposed for ICI therapies but have not been incorporated into Australian clinical practice guidelines. Further research, validation, and assessment of clinical utility is required before more prognostic and predictive biomarkers are fluidly integrated into routine care.
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Affiliation(s)
- Nigel G Maher
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ismael A Vergara
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.
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4
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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] [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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5
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Ahn SY, Bae GE, Park SY, Yeo MK. Differences in the Clinical and Molecular Profiles of Subungual Melanoma and Acral Melanoma in Asian Patients. Cancers (Basel) 2023; 15:4417. [PMID: 37686691 PMCID: PMC10486359 DOI: 10.3390/cancers15174417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Subungual melanoma (SUM) is a rare type of malignant melanoma that arises beneath the nails. SUM is categorized as a type of acral melanoma (AM), which occurs on the hands and feet. SUM is an aggressive type of cutaneous melanoma that is most common among Asian patients. Recent studies reveal that SUM and AM might have different molecular characteristics. Treatment of melanoma relies on analysis of both clinical and molecular data. Therefore, the clinical and molecular characteristics of SUM need to be established, especially during metastasis. To define the mutation profiles of SUM and compare them with those of AM, we performed next-generation sequencing of primary and metastatic tumors of SUM and AM patients. Subungual location was a better independent prognostic factor than acral location for better overall survival (p = 0.001). Patients with SUM most commonly had the triple wild-type (75%) driven by GNAQ (58%) and KIT (25%) mutations, whereas patients with AM had BRAF (28.6%) and RAF (14.3%) molecular types of mutations. Single-nucleotide variations (SNVs) were more common in SUM than in AM, whereas copy number alterations (CNAs) were more common metastatic lesions of AM. Metastatic tumors in patients with SUM and AM showed increases in CNAs (43% and 80%, respectively), but not in SNVs. The number of CNAs increased during metastasis. When compared with AM, SUM has distinct clinical and molecular characteristics.
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Affiliation(s)
- So-Young Ahn
- Department of Rehabilitation Medicine, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea;
| | - Go-Eun Bae
- Department of Pathology, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea;
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Gyeongbuk, Republic of Korea
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea;
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Yang TT, Yu S, Ke CLK, Cheng ST. The Genomic Landscape of Melanoma and Its Therapeutic Implications. Genes (Basel) 2023; 14:genes14051021. [PMID: 37239381 DOI: 10.3390/genes14051021] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/25/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Melanoma is one of the most aggressive malignancies of the skin. The genetic composition of melanoma is complex and varies among different subtypes. With the aid of recent technologies such as next generation sequencing and single-cell sequencing, our understanding of the genomic landscape of melanoma and its tumor microenvironment has become increasingly clear. These advances may provide explanation to the heterogenic treatment outcomes of melanoma patients under current therapeutic guidelines and provide further insights to the development of potential new therapeutic targets. Here, we provide a comprehensive review on the genetics related to melanoma tumorigenesis, metastasis, and prognosis. We also review the genetics affecting the melanoma tumor microenvironment and its relation to tumor progression and treatment.
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Affiliation(s)
- Ting-Ting Yang
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Dermatology, Pingtung Hospital, Ministry of Health and Welfare, Pingtung 900, Taiwan
| | - Sebastian Yu
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Dermatology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chiao-Li Khale Ke
- Department of Psychiatry, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Psychiatry, Kaohsiung Municipal SiaoGang Hospital, Kaohsiung Medical University, Kaohsiung 812, Taiwan
| | - Shih-Tsung Cheng
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Dermatology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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7
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Li Y, Wang B, Wang C, Zhao D, Liu Z, Niu Y, Wang X, Li W, Zhu J, Tao H, Ma T, Li T. Genomic and Transcriptional Profiling of Chinese Melanoma Patients Enhanced Potentially Druggable Targets: A Multicenter Study. Cancers (Basel) 2022; 15:cancers15010283. [PMID: 36612279 PMCID: PMC9818204 DOI: 10.3390/cancers15010283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND In contrast to Caucasian melanoma, which has been extensively studied, there are few studies on melanoma in Asian populations. Sporadic studies reported that only 40% of Asian melanoma patients could be druggable, which was much lower than that in Caucasians. More studies are required to refine this conclusion. METHODS Chinese melanoma patients (n = 469) were sequentially sequenced by DNA-NGS and RNA-NGS. The genomic alterations were determined, and potentially actionable targets were investigated. RESULTS Patients with potential druggable targets were identified in 75% of Chinese melanoma patients by DNA-NGS based on OncoKB, which was much higher than in a previous Asian study. NRG1 fusions were first identified in melanoma. In addition, up to 11.7% (7/60) of patients in the undruggable group could be recognized as actionable by including RNA-NGS analysis. By comparing the fusion detection rate between DNA-NGS and RNA-NGS, all available samples after DNA-NGS detection were further verified by RNA-NGS. The use of RNA-NGS enhanced the proportion of druggable fusions from 2.56% to 17.27%. In total, the use of RNA-NGS increased the druggable proportion from 75% to 78%. CONCLUSIONS In this study, we systemically analyzed the actionable landscape of melanoma in the largest Asian cohort. In addition, we first demonstrated how DNA and RNA sequential sequencing is essential in bringing clinical benefits to more patients with melanoma.
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Affiliation(s)
- Yue Li
- Harbin Medical University Cancer Hospital, Harbin 150040, China
| | - Baoming Wang
- Jichenjunchuang Clinical Laboratory, Hangzhou 310022, China
| | - Chunyang Wang
- Jichenjunchuang Clinical Laboratory, Hangzhou 310022, China
| | - Dandan Zhao
- Jichenjunchuang Clinical Laboratory, Hangzhou 310022, China
| | - Zhengchuang Liu
- Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Yanling Niu
- Jichenjunchuang Clinical Laboratory, Hangzhou 310022, China
| | - Xiaojuan Wang
- Jichenjunchuang Clinical Laboratory, Hangzhou 310022, China
| | - Wei Li
- Jichenjunchuang Clinical Laboratory, Hangzhou 310022, China
| | - Jianhua Zhu
- Jichenjunchuang Clinical Laboratory, Hangzhou 310022, China
| | - Houquan Tao
- Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, China
- Department of Surgery, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Tonghui Ma
- Jichenjunchuang Clinical Laboratory, Hangzhou 310022, China
- Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou 310014, China
- Correspondence: (T.M.); (T.L.)
| | - Tao Li
- Institute of Basic Medicine and Cancer (IBMC), Department of Bone and Soft-tissue Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310022, China
- Correspondence: (T.M.); (T.L.)
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8
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Sun W, Zhao F, Hu T, Wu Z, Xu Y, Dong Y, Zheng B, Wang C, Yan W, Zhu X, Wu J, McKay MJ, Arozarena I, Alos L, Teixido C, Chen Y. Oncogenic alterations reveal key strategies for precision oncology in melanoma treatment. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1246. [PMID: 36544693 PMCID: PMC9761125 DOI: 10.21037/atm-22-5346] [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: 10/27/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022]
Abstract
Background Molecular profiling with next-generation sequencing (NGS) has been applied in multiple solid tumors, including melanomas, to identify potential drug targets. However, the association between clinical outcomes and the molecular alterations has not yet been fully clarified. Methods A total of 108 patients with melanoma were included in this study, 95 of whom had both sequencing data and clinical outcomes were collected. We analyzed the genetic alterations of 108 malignant melanoma patients using the OncoCare panel, which covers 559 genes. Results A model was also established to predict side effects through a combination analysis of clinical data and somatic variants, yielding an area under the receiver operating characteristic curve (AUROC) score of 0.8. We also identified epidermal growth factor receptor (EGFR) mutation was excellent predictor for progression-free survival (PFS) for patient who received immunotherapy (log-rank P=0.01), while tumor mutation burden (TMB) was found to not be significantly associated with PFS (log-rank P=0.87). Combining clinical features with genetic analysis, we found that patients carrying both DNA POLD1/ALOX12B or POLD1/PTPRT mutations had a significantly lower survival rate. Conclusions Overall, these results demonstrate the benefits of applying NGS clinical panels and shed light on future directions of personalized therapeutics for the treatment of melanoma.
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Affiliation(s)
- Wei Sun
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fang Zhao
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Tu Hu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Wu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Xu
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Dong
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Biqiang Zheng
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunmeng Wang
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wangjun Yan
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoli Zhu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China;,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jian Wu
- MyGenostics Inc., Beijing, China
| | - Michael J. McKay
- Department of Radiation Oncology, Northern Cancer Service, Burnie, Australia
| | - Imanol Arozarena
- Navarrabiomed-Fundación Miguel Servet-Idisna, Complejo Hospitalario de Navarra, Pamplona, Spain
| | - Llucia Alos
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Cristina Teixido
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Yong Chen
- Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai, China;,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Hong ES, Messersmith WA, Hammad H, Cornish TC, Aisner DL. Tissue Displacement Versus Two Primary Colorectal Carcinomas? A Case Report on the Utility of Comparative Sequencing. JCO Precis Oncol 2022; 6:e2200252. [PMID: 36240469 PMCID: PMC9616644 DOI: 10.1200/po.22.00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/01/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023] Open
Affiliation(s)
- Ellie S. Hong
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO
| | - Wells A. Messersmith
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Hazem Hammad
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Toby C. Cornish
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO
| | - Dara L. Aisner
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO
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10
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Wang Z, Zhang T, Wu W, Wu L, Li J, Huang B, Liang Y, Li Y, Li P, Li K, Wang W, Guo R, Wang Q. Detection and Localization of Solid Tumors Utilizing the Cancer-Type-Specific Mutational Signatures. Front Bioeng Biotechnol 2022; 10:883791. [PMID: 35547159 PMCID: PMC9081532 DOI: 10.3389/fbioe.2022.883791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Accurate detection and location of tumor lesions are essential for improving the diagnosis and personalized cancer therapy. However, the diagnosis of lesions with fuzzy histology is mainly dependent on experiences and with low accuracy and efficiency. Here, we developed a logistic regression model based on mutational signatures (MS) for each cancer type to trace the tumor origin. We observed MS could distinguish cancer from inflammation and healthy individuals. By collecting extensive datasets of samples from ten tumor types in the training cohort (5,001 samples) and independent testing cohort (2,580 samples), cancer-type-specific MS patterns (CTS-MS) were identified and had a robust performance in distinguishing different types of primary and metastatic solid tumors (AUC:0.76 ∼ 0.93). Moreover, we validated our model in an Asian population and found that the AUC of our model in predicting the tumor origin of the Asian population was higher than 0.7. The metastatic tumor lesions inherited the MS pattern of the primary tumor, suggesting the capability of MS in identifying the tissue-of-origin for metastatic cancers. Furthermore, we distinguished breast cancer and prostate cancer with 90% accuracy by combining somatic mutations and CTS-MS from cfDNA, indicating that the CTS-MS could improve the accuracy of cancer-type prediction by cfDNA. In summary, our study demonstrated that MS was a novel reliable biomarker for diagnosing solid tumors and provided new insights into predicting tissue-of-origin.
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Affiliation(s)
- Ziyu Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Tingting Zhang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Lingxiang Wu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Jie Li
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Bin Huang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Yuan Liang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Yan Li
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Pengping Li
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Kening Li
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Kening Li, ; Wei Wang, ; Renhua Guo, ; Qianghu Wang,
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Kening Li, ; Wei Wang, ; Renhua Guo, ; Qianghu Wang,
| | - Renhua Guo
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Kening Li, ; Wei Wang, ; Renhua Guo, ; Qianghu Wang,
| | - Qianghu Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Kening Li, ; Wei Wang, ; Renhua Guo, ; Qianghu Wang,
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11
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Yoon S, Kim M, Hong YS, Kim HS, Kim ST, Kim J, Yun H, Yoo C, Ahn HK, Kim HS, Lee IH, Kim IH, Park I, Jeong JH, Cheon J, Kim JW, Yun J, Lim SM, Cha Y, Jang SJ, Zang DY, Kim TW, Kang JH, Kim JH. Recommendations for the Use of Next-Generation Sequencing and the Molecular Tumor Board for Patients with Advanced Cancer: A Report from KSMO and KCSG Precision Medicine Networking Group. Cancer Res Treat 2021; 54:1-9. [PMID: 34902959 PMCID: PMC8756119 DOI: 10.4143/crt.2021.1115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/08/2021] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing (NGS) is becoming essential in the fields of precision oncology. With implementation of NGS in daily clinic, the needs for continued education, facilitated interpretation of NGS results and optimal treatment delivery based on NGS results have been addressed. Molecular tumor board (MTB) is multidisciplinary approach to keep pace with the growing knowledge of complex molecular alterations in patients with advanced solid cancer. Although guidelines for NGS use and MTB have been developed in western countries, there is limitation for reflection of Korea’s public health environment and daily clinical practice. These recommendations provide a critical guidance from NGS panel testing to final treatment decision based on MTB discussion.
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Affiliation(s)
- Shinkyo Yoon
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yong Sang Hong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Han Sang Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, College of Medicine, Seoul, Korea
| | - Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hee Kyung Ahn
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Hyo Song Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - In Hee Lee
- Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - In-Ho Kim
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Inkeun Park
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Jae Ho Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jaekyung Cheon
- Department of Medical Oncology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea
| | - Jin Won Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Jina Yun
- Division of Medical Oncology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Sun Min Lim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Yongjun Cha
- Center for Colorectal Cancer, National Cancer Center, Research Institute and Hospital, Goyang, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Dae Young Zang
- Department of Internal Medicine, Hallym University Medical Center, Hallym University, Anyang, Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Hyoung Kang
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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12
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Ronchi A, Montella M, Zito Marino F, Caraglia M, Grimaldi A, Argenziano G, Moscarella E, Brancaccio G, Troiani T, Napolitano S, Franco R, Cozzolino I. Predictive Evaluation on Cytological Sample of Metastatic Melanoma: The Role of BRAF Immunocytochemistry in the Molecular Era. Diagnostics (Basel) 2021; 11:diagnostics11061110. [PMID: 34207125 PMCID: PMC8235421 DOI: 10.3390/diagnostics11061110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cutaneous malignant melanoma is an aggressive neoplasm. In advanced cases, the therapeutic choice depends on the mutational status of BRAF. Fine needle aspiration cytology (FNA) is often applied to the management of patients affected by melanoma, mainly for the diagnosis of metastases. The evaluation of BRAF mutational status by sequencing technique on cytological samples may be inconvenient, as it is a time and biomaterial-consuming technique. Recently, BRAF immunocytochemistry (ICC) was applied for the evaluation of BRAF V600E mutational status. Although it may be useful mainly in cytological samples, data about BRAF ICC on cytological samples are missing. METHODS We performed BRAF ICC on a series of 50 FNA samples of metastatic melanoma. BRAF molecular analysis was performed on the same cytological samples or on the corresponding histological samples. Molecular analysis was considered the gold standard. RESULTS BRAF ICC results were adequate in 49 out of 50 (98%) cases, positive in 15 out of 50 (30%) cases and negative in 34 out of 50 (68%) of cases. Overall, BRAF ICC sensitivity, specificity, positive predictive value and negative predictive value results were 88.2%, 100%, 100% and 94.1%, respectively. The diagnostic performance of BRAF ICC results was perfect when molecular evaluation was performed on the same cytological samples. Hyperpigmentation represents the main limitation of the technique. CONCLUSIONS BRAF ICC is a rapid, cost-effective method for detecting BRAF V600E mutation in melanoma metastases, applicable with high diagnostic performance to cytological samples. It could represent the first step to evaluate BRAF mutational status in cytological samples, mainly in poorly cellular cases.
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Affiliation(s)
- Andrea Ronchi
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.M.); (F.Z.M.); (I.C.)
- Correspondence: (A.R.); (R.F.)
| | - Marco Montella
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.M.); (F.Z.M.); (I.C.)
| | - Federica Zito Marino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.M.); (F.Z.M.); (I.C.)
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.C.); (A.G.)
| | - Anna Grimaldi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.C.); (A.G.)
| | - Giuseppe Argenziano
- Dermatology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (G.A.); (E.M.); (G.B.)
| | - Elvira Moscarella
- Dermatology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (G.A.); (E.M.); (G.B.)
| | - Gabriella Brancaccio
- Dermatology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (G.A.); (E.M.); (G.B.)
| | - Teresa Troiani
- Oncology Unit, Department of Precision Medicine, Università della Campania “Luigi Vanvitelli”, 80131 Naples, Italy; (T.T.); (S.N.)
| | - Stefania Napolitano
- Oncology Unit, Department of Precision Medicine, Università della Campania “Luigi Vanvitelli”, 80131 Naples, Italy; (T.T.); (S.N.)
| | - Renato Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.M.); (F.Z.M.); (I.C.)
- Correspondence: (A.R.); (R.F.)
| | - Immacolata Cozzolino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.M.); (F.Z.M.); (I.C.)
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13
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Scatena C, Murtas D, Tomei S. Cutaneous Melanoma Classification: The Importance of High-Throughput Genomic Technologies. Front Oncol 2021; 11:635488. [PMID: 34123788 PMCID: PMC8193952 DOI: 10.3389/fonc.2021.635488] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Cutaneous melanoma is an aggressive tumor responsible for 90% of mortality related to skin cancer. In the recent years, the discovery of driving mutations in melanoma has led to better treatment approaches. The last decade has seen a genomic revolution in the field of cancer. Such genomic revolution has led to the production of an unprecedented mole of data. High-throughput genomic technologies have facilitated the genomic, transcriptomic and epigenomic profiling of several cancers, including melanoma. Nevertheless, there are a number of newer genomic technologies that have not yet been employed in large studies. In this article we describe the current classification of cutaneous melanoma, we review the current knowledge of the main genetic alterations of cutaneous melanoma and their related impact on targeted therapies, and we describe the most recent high-throughput genomic technologies, highlighting their advantages and disadvantages. We hope that the current review will also help scientists to identify the most suitable technology to address melanoma-related relevant questions. The translation of this knowledge and all actual advancements into the clinical practice will be helpful in better defining the different molecular subsets of melanoma patients and provide new tools to address relevant questions on disease management. Genomic technologies might indeed allow to better predict the biological - and, subsequently, clinical - behavior for each subset of melanoma patients as well as to even identify all molecular changes in tumor cell populations during disease evolution toward a real achievement of a personalized medicine.
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Affiliation(s)
- Cristian Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Daniela Murtas
- Department of Biomedical Sciences, Section of Cytomorphology, University of Cagliari, Cagliari, Italy
| | - Sara Tomei
- Omics Core, Integrated Genomics Services, Research Department, Sidra Medicine, Doha, Qatar
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14
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Angus L, Starmans MPA, Rajicic A, Odink AE, Jalving M, Niessen WJ, Visser JJ, Sleijfer S, Klein S, van der Veldt AAM. The BRAF P.V600E Mutation Status of Melanoma Lung Metastases Cannot Be Discriminated on Computed Tomography by LIDC Criteria nor Radiomics Using Machine Learning. J Pers Med 2021; 11:257. [PMID: 33915880 PMCID: PMC8066683 DOI: 10.3390/jpm11040257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 11/05/2022] Open
Abstract
Patients with BRAF mutated (BRAF-mt) metastatic melanoma benefit significantly from treatment with BRAF inhibitors. Currently, the BRAF status is determined on archival tumor tissue or on fresh tumor tissue from an invasive biopsy. The aim of this study was to evaluate whether radiomics can predict the BRAF status in a non-invasive manner. Patients with melanoma lung metastases, known BRAF status, and a pretreatment computed tomography scan were included. After semi-automatic annotation of the lung lesions (maximum two per patient), 540 radiomics features were extracted. A chest radiologist scored all segmented lung lesions according to the Lung Image Database Consortium (LIDC) criteria. Univariate analysis was performed to assess the predictive value of each feature for BRAF mutation status. A combination of various machine learning methods was used to develop BRAF decision models based on the radiomics features and LIDC criteria. A total of 169 lung lesions from 103 patients (51 BRAF-mt; 52 BRAF wild type) were included. There were no features with a significant discriminative value in the univariate analysis. Models based on radiomics features and LIDC criteria both performed as poorly as guessing. Hence, the BRAF mutation status in melanoma lung metastases cannot be predicted using radiomics features or visually scored LIDC criteria.
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Affiliation(s)
- Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (A.R.); (S.S.); (A.A.M.v.d.V.)
- Department of Radiology and Nuclear Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (M.P.A.S.); (A.E.O.); (W.J.N.); (J.J.V.); (S.K.)
| | - Martijn P. A. Starmans
- Department of Radiology and Nuclear Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (M.P.A.S.); (A.E.O.); (W.J.N.); (J.J.V.); (S.K.)
- Department of Medical Informatics, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Ana Rajicic
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (A.R.); (S.S.); (A.A.M.v.d.V.)
| | - Arlette E. Odink
- Department of Radiology and Nuclear Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (M.P.A.S.); (A.E.O.); (W.J.N.); (J.J.V.); (S.K.)
| | - Mathilde Jalving
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Wiro J. Niessen
- Department of Radiology and Nuclear Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (M.P.A.S.); (A.E.O.); (W.J.N.); (J.J.V.); (S.K.)
- Department of Medical Informatics, Erasmus MC, 3015 GD Rotterdam, The Netherlands
- Faculty of Applied Sciences, Delft University of Technology, 2628 CJ Delft, The Netherlands
| | - Jacob J. Visser
- Department of Radiology and Nuclear Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (M.P.A.S.); (A.E.O.); (W.J.N.); (J.J.V.); (S.K.)
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (A.R.); (S.S.); (A.A.M.v.d.V.)
| | - Stefan Klein
- Department of Radiology and Nuclear Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (M.P.A.S.); (A.E.O.); (W.J.N.); (J.J.V.); (S.K.)
- Department of Medical Informatics, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Astrid A. M. van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (A.R.); (S.S.); (A.A.M.v.d.V.)
- Department of Radiology and Nuclear Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (M.P.A.S.); (A.E.O.); (W.J.N.); (J.J.V.); (S.K.)
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15
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Palma SD, McConnell A, Verganti S, Starkey M. Review on Canine Oral Melanoma: An Undervalued Authentic Genetic Model of Human Oral Melanoma? Vet Pathol 2021; 58:881-889. [PMID: 33685309 DOI: 10.1177/0300985821996658] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Oral melanoma (OM) is a highly aggressive tumor of the oral cavity in humans and dogs. Here we review the phenotypic similarities between the disease in these 2 species as the basis for the view that canine OM is a good model for the corresponding human disease. Utility of the "canine model" has likely been hindered by a paucity of information about the extent of the molecular genetic similarities between human and canine OMs. Current knowledge of the somatic alterations that underpin human tumorigenesis and metastatic progression is relatively limited, primarily due to the rarity of the disease in humans and consequent lack of opportunity for large-scale molecular analysis. The molecular genetic comparisons between human and canine OMs that have been completed indicate some overlap between the somatic mutation profiles of canine OMs and a subset of human OMs. However, further comparative studies featuring, in particular, larger numbers of human OMs are required to provide substantive evidence that canine OMs share mechanisms of tumorigenesis with at least a subset of human OMs. Future molecular genetic investigations of both human and canine OMs should investigate how primary tumors develop a metastatic gene expression signature and the genetic and epigenetic alterations specific to metastatic sites. Such studies may identify genetic alterations and pathways specific to the metastatic disease which could be targetable by new drugs.
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Affiliation(s)
| | | | - Sara Verganti
- 170851Dick White Referrals, Station Farm, Cambridgeshire, UK
| | - Mike Starkey
- 11661Animal Health Trust, Newmarket, Suffolk, UK
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16
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Makohon-Moore AP, Lipson EJ, Hooper JE, Zucker A, Hong J, Bielski CM, Hayashi A, Tokheim C, Baez P, Kappagantula R, Kohutek Z, Makarov V, Riaz N, Postow MA, Chapman PB, Karchin R, Socci ND, Solit DB, Chan TA, Taylor BS, Topalian SL, Iacobuzio-Donahue CA. The Genetic Evolution of Treatment-Resistant Cutaneous, Acral, and Uveal Melanomas. Clin Cancer Res 2021; 27:1516-1525. [PMID: 33323400 PMCID: PMC7925434 DOI: 10.1158/1078-0432.ccr-20-2984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/21/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Melanoma is a biologically heterogeneous disease composed of distinct clinicopathologic subtypes that frequently resist treatment. To explore the evolution of treatment resistance and metastasis, we used a combination of temporal and multilesional tumor sampling in conjunction with whole-exome sequencing of 110 tumors collected from 7 patients with cutaneous (n = 3), uveal (n = 2), and acral (n = 2) melanoma subtypes. EXPERIMENTAL DESIGN Primary tumors, metastases collected longitudinally, and autopsy tissues were interrogated. All but 1 patient died because of melanoma progression. RESULTS For each patient, we generated phylogenies and quantified the extent of genetic diversity among tumors, specifically among putative somatic alterations affecting therapeutic resistance. CONCLUSIONS In 4 patients who received immunotherapy, we found 1-3 putative acquired and intrinsic resistance mechanisms coexisting in the same patient, including mechanisms that were shared by all tumors within each patient, suggesting that future therapies directed at overcoming intrinsic resistance mechanisms may be broadly effective.
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Affiliation(s)
- Alvin P Makohon-Moore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Evan J Lipson
- Johns Hopkins Bloomberg-Kimmel Institute for Cancer Immunotherapy, Kimmel Cancer Center, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jody E Hooper
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Amanda Zucker
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jungeui Hong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Akimasa Hayashi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Kyorin University, Mitaka City, Tokyo, Japan
| | - Collin Tokheim
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Priscilla Baez
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rajya Kappagantula
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zachary Kohutek
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nadeem Riaz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael A Postow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Paul B Chapman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rachel Karchin
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Nicholas D Socci
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Suzanne L Topalian
- Johns Hopkins Bloomberg-Kimmel Institute for Cancer Immunotherapy, Kimmel Cancer Center, Baltimore, Maryland.
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine A Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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17
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Fois SS, Paliogiannis P, Zinellu A, Fois AG, Cossu A, Palmieri G. Molecular Epidemiology of the Main Druggable Genetic Alterations in Non-Small Cell Lung Cancer. Int J Mol Sci 2021; 22:ijms22020612. [PMID: 33435440 PMCID: PMC7827915 DOI: 10.3390/ijms22020612] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/30/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is the leading cause of death for malignancy worldwide. Its molecular profiling has enriched our understanding of cancer initiation and progression and has become fundamental to provide guidance on treatment with targeted therapies. Testing the presence of driver mutations in specific genes in lung tumors has thus radically changed the clinical management and outcomes of the disease. Numerous studies performed with traditional sequencing methods have investigated the occurrence of such mutations in lung cancer, and new insights regarding their frequency and clinical significance are continuously provided with the use of last generation sequencing technologies. In this review, we discuss the molecular epidemiology of the main druggable genetic alterations in non-small cell lung cancer, namely EGFR, KRAS, BRAF, MET, and HER2 mutations or amplification, as well as ALK and ROS1 fusions. Furthermore, we investigated the predictive impact of these alterations on the outcomes of modern targeted therapies, their global prognostic significance, and their mutual interaction in cases of co-occurrence.
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Affiliation(s)
- Sara S. Fois
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Viale San Pietro 43, 07100 Sassari, Italy; (S.S.F.); (A.G.F.); (A.C.)
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Viale San Pietro 43, 07100 Sassari, Italy; (S.S.F.); (A.G.F.); (A.C.)
- Correspondence: ; Tel.: +39-340-593-1590
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy;
| | - Alessandro G. Fois
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Viale San Pietro 43, 07100 Sassari, Italy; (S.S.F.); (A.G.F.); (A.C.)
| | - Antonio Cossu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Viale San Pietro 43, 07100 Sassari, Italy; (S.S.F.); (A.G.F.); (A.C.)
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy;
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18
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Vanni I, Casula M, Pastorino L, Manca A, Dalmasso B, Andreotti V, Pisano M, Colombino M, Pfeffer U, Tanda ET, Rozzo C, Paliogiannis P, Cossu A, Ghiorzo P, Palmieri G. Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI). Diagn Pathol 2020; 15:143. [PMID: 33317587 PMCID: PMC7737361 DOI: 10.1186/s13000-020-01052-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Identification of somatic mutations in key oncogenes in melanoma is important to lead the effective and efficient use of personalized anticancer treatment. Conventional methods focus on few genes per run and, therefore, are unable to screen for multiple genes simultaneously. The use of Next-Generation Sequencing (NGS) technologies enables sequencing of multiple cancer-driving genes in a single assay, with reduced costs and DNA quantity needed and increased mutation detection sensitivity. METHODS We designed a customized IMI somatic gene panel for targeted sequencing of actionable melanoma mutations; this panel was tested on three different NGS platforms using 11 metastatic melanoma tissue samples in blinded manner between two EMQN quality certificated laboratory. RESULTS The detection limit of our assay was set-up to a Variant Allele Frequency (VAF) of 10% with a coverage of at least 200x. All somatic variants detected by all NGS platforms with a VAF ≥ 10%, were also validated by an independent method. The IMI panel achieved a very good concordance among the three NGS platforms. CONCLUSION This study demonstrated that, using the main sequencing platforms currently available in the diagnostic setting, the IMI panel can be adopted among different centers providing comparable results.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Milena Casula
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Antonella Manca
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Bruna Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Marina Pisano
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Maria Colombino
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Ulrich Pfeffer
- Tumor Epigenetics, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Carla Rozzo
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Cossu
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy.
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy.
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
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19
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Loo K, Gauvin G, Soliman I, Renzetti M, Deng M, Ross E, Luo B, Wu H, Reddy S, Olszanski AJ, Farma JM. Primary tumor characteristics and next-generation sequencing mutations as biomarkers for melanoma immunotherapy response. Pigment Cell Melanoma Res 2020; 33:878-888. [PMID: 32564504 DOI: 10.1111/pcmr.12909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/28/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Considerable advances in melanoma have been realized through immunotherapy. The principal aim was to determine whether primary tumor characteristics or next-generation sequencing (NGS) could serve as markers of immunotherapy response. METHODS AND RESULTS The study cohort consisted of 67 patients who received immunotherapy for recurrent or metastatic melanoma and for whom primary tumor biopsies and pathology reports were available. A subset of 59 patient tumors were profiled using an NGS panel of 50 cancer-related genes. Objective response rate to immunotherapy was assessed using RECIST v1.1 criteria. Progression-free survival (PFS) and overall survival (OS) were used as endpoints. Lymphovascular invasion (LVI) strongly correlated with an increased proportion of immunotherapy responders (p = .002). PFS interval (p = .003) and OS (p = .036) were significantly higher in patients with LVI. NRAS mutation was more strongly correlated with an increased proportion of immunotherapy responders (p =.050). PFS was significantly higher in patients with NRAS mutation (p = .042); no difference in OS (p = .111). DISCUSSION This analysis demonstrates an association between lymphovascular invasion and immunotherapy response. Additionally, NGS mutation analysis demonstrated a potential association between NRAS mutations and immunotherapy response.
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Affiliation(s)
- Kimberly Loo
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA.,Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Gabrielle Gauvin
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Iman Soliman
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Madelyn Renzetti
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA.,Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Mengying Deng
- Department of Statistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Eric Ross
- Department of Statistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Biao Luo
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Hong Wu
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Sanjay Reddy
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Anthony J Olszanski
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jeffrey M Farma
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
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20
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Rao S, Pitel B, Wagner AH, Boca SM, McCoy M, King I, Gupta S, Park BH, Warner JL, Chen J, Rogan PK, Chakravarty D, Griffith M, Griffith OL, Madhavan S. Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices. JCO Clin Cancer Inform 2020; 4:602-613. [PMID: 32644817 PMCID: PMC7397775 DOI: 10.1200/cci.19.00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The cancer research community is constantly evolving to better understand tumor biology, disease etiology, risk stratification, and pathways to novel treatments. Yet the clinical cancer genomics field has been hindered by redundant efforts to meaningfully collect and interpret disparate data types from multiple high-throughput modalities and integrate into clinical care processes. Bespoke data models, knowledgebases, and one-off customized resources for data analysis often lack adequate governance and quality control needed for these resources to be clinical grade. Many informatics efforts focused on genomic interpretation resources for neoplasms are underway to support data collection, deposition, curation, harmonization, integration, and analytics to support case review and treatment planning. METHODS In this review, we evaluate and summarize the landscape of available tools, resources, and evidence used in the evaluation of somatic and germline tumor variants within the context of molecular tumor boards. RESULTS Molecular tumor boards (MTBs) are collaborative efforts of multidisciplinary cancer experts equipped with genomic interpretation resources to aid in the delivery of accurate and timely clinical interpretations of complex genomic results for each patient, within an institution or hospital network. Virtual MTBs (VMTBs) provide an online forum for collaborative governance, provenance, and information sharing between experts outside a given hospital network with the potential to enhance MTB discussions. Knowledge sharing in VMTBs and communication with guideline-developing organizations can lead to progress evidenced by data harmonization across resources, crowd-sourced and expert-curated genomic assertions, and a more informed and explainable usage of artificial intelligence. CONCLUSION Advances in cancer genomics interpretation aid in better patient and disease classification, more streamlined identification of relevant literature, and a more thorough review of available treatments and predicted patient outcomes.
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Affiliation(s)
- Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Beth Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Alex H. Wagner
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Simina M. Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Matthew McCoy
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Ian King
- Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Samir Gupta
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Ben Ho Park
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Jeremy L. Warner
- Departments of Medicine and Biomedical Informatics, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - James Chen
- Division of Medical Oncology, Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Peter K. Rogan
- Departments of Biochemistry and Oncology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Debyani Chakravarty
- Kravis Center of Molecular Oncology, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Malachi Griffith
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Obi L. Griffith
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
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21
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Detection of Gene Mutations in Liquid Biopsy of Melanoma Patients: Overview and Future Perspectives. Curr Treat Options Oncol 2020; 21:19. [PMID: 32048063 DOI: 10.1007/s11864-020-0708-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OPINION STATEMENT Liquid biopsies are still far from widely implanted in the clinical arena. Issues related to the added sensitivity of this test beyond conventional methods have not been fully resolved. Additionally, issues related to the specificity of these results especially as many cancers may share common mutation need further investigations. One way to resolve this may include the development and testing of large gene panels to add higher specificity. On the other hand, further studies are needed to support the idea that ctDNA or circulating tumor cells may constitute a better representation of the tumor subpopulation that is capable of metastasizing, which will strongly support its clinical value. Finally, survival studies showing a positive impact of this technology will also justify its widespread implementation in clinical practice.
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22
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Betancourt LH, Szasz AM, Kuras M, Rodriguez Murillo J, Sugihara Y, Pla I, Horvath Z, Pawłowski K, Rezeli M, Miharada K, Gil J, Eriksson J, Appelqvist R, Miliotis T, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Welinder C, Wieslander E, Kwon HJ, Malm J, Nemeth IB, Jönsson G, Fenyö D, Sanchez A, Marko-Varga G. The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes. Cancers (Basel) 2019; 11:E1981. [PMID: 31835364 PMCID: PMC6966659 DOI: 10.3390/cancers11121981] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/23/2019] [Accepted: 12/03/2019] [Indexed: 02/07/2023] Open
Abstract
In comparison to other human cancer types, malignant melanoma exhibits the greatest amount of heterogeneity. After DNA-based detection of the BRAF V600E mutation in melanoma patients, targeted inhibitor treatment is the current recommendation. This approach, however, does not take the abundance of the therapeutic target, i.e., the B-raf V600E protein, into consideration. As shown by immunohistochemistry, the protein expression profiles of metastatic melanomas clearly reveal the existence of inter- and intra-tumor variability. Nevertheless, the technique is only semi-quantitative. To quantitate the mutant protein there is a fundamental need for more precise techniques that are aimed at defining the currently non-existent link between the levels of the target protein and subsequent drug efficacy. Using cutting-edge mass spectrometry combined with DNA and mRNA sequencing, the mutated B-raf protein within metastatic tumors was quantitated for the first time. B-raf V600E protein analysis revealed a subjacent layer of heterogeneity for mutation-positive metastatic melanomas. These were characterized into two distinct groups with different tumor morphologies, protein profiles and patient clinical outcomes. This study provides evidence that a higher level of expression in the mutated protein is associated with a more aggressive tumor progression. Our study design, comprised of surgical isolation of tumors, histopathological characterization, tissue biobanking, and protein analysis, may enable the eventual delineation of patient responders/non-responders and subsequent therapy for malignant melanoma.
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Affiliation(s)
- Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - A. Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
- Cancer Center, Semmelweis University, Budapest 1083, Hungary
| | - Magdalena Kuras
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Jimmy Rodriguez Murillo
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden; (J.R.M.); (Y.S.)
| | - Yutaka Sugihara
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden; (J.R.M.); (Y.S.)
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Krzysztof Pawłowski
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Kenichi Miharada
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, Sölvegatan 17, 221 84 Lund, Sweden;
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Tasso Miliotis
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, 431 50 Gothenburg, Sweden;
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, Skåne University Hospital, 222 42 Lund, Sweden;
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, 9712 CP Groningen, The Netherlands;
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul 03722, Korea;
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Istvan Balazs Nemeth
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary;
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, 550 1st Ave, New York, NY 10016, USA;
| | - Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
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23
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Colombino M, Paliogiannis P, Cossu A, De Re V, Miolo G, Botti G, Scognamiglio G, Ascierto PA, Santeufemia DA, Fraggetta F, Manca A, Sini MC, Casula M, Palomba G, Pisano M, Doneddu V, Lissia A, Fedeli MA, Palmieri G. BRAF Mutations and Dysregulation of the MAP Kinase Pathway Associated to Sinonasal Mucosal Melanomas. J Clin Med 2019; 8:jcm8101577. [PMID: 31581559 PMCID: PMC6832198 DOI: 10.3390/jcm8101577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 09/16/2019] [Accepted: 09/24/2019] [Indexed: 12/03/2022] Open
Abstract
Sinonasal mucosal melanoma (SNM) is a rare and aggressive type of melanoma, and because of this, we currently have a limited understanding of its genetic and molecular constitution. The incidence among SNMs of somatic mutations in the genes involved in the main molecular pathways, which have been largely associated with cutaneous melanoma, is not yet fully understood. Through a next-generation sequencing (NGS) approach using a panel of 25 genes involved in melanoma pathogenesis customized by our group, we performed a mutation analysis in a cohort of 25 SNM patients. Results showed that pathogenic mutations were found in more than 60% of SNM cases at a somatic level, with strikingly 32% of them carrying deleterious mutations in the BRAF gene. The identified mutations mostly lack the typical UV signature associated with cutaneous melanomas and showed no significant association with any histopathological parameter. Oncogenic activation of the BRAF-depending pathway, which may induce immune tolerance into the tumour microenvironment (i.e., by increasing the VEGF production) was poorly associated with mutations in genes that have been related to diminished clinical benefit of the treatment with BRAF inhibitors. Screening for mutations in BRAF and other MAPK genes should be included in the routine diagnostic test for a better classification of SNM patients.
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Affiliation(s)
- Maria Colombino
- Institute of Biomolecular Chemistry, National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Viale S., 07100 Sassari, Italy.
| | - Antonio Cossu
- Anatomia Patologica, Azienda Ospedaliero Universitaria (AOU), 07100 Sassari, Italy.
| | - Valli De Re
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico (CRO), 33081 Pordenone, Italy.
| | - Gianmaria Miolo
- Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), 33081 Pordenone, Italy.
| | - Gerardo Botti
- Istituto Nazionale Tumori "Fondazione Pascale", 80131 Naples, Italy.
| | | | | | | | - Filippo Fraggetta
- Anatomia Patologica, Azienda Ospedaliera Cannizzaro, Via Messina 829, 95126 Catania, Italy.
| | - Antonella Manca
- Institute of Biomolecular Chemistry, National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
| | - Maria Cristina Sini
- Institute of Biomolecular Chemistry, National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
| | - Milena Casula
- Institute of Biomolecular Chemistry, National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
| | - Grazia Palomba
- Institute of Biomolecular Chemistry, National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
| | - Marina Pisano
- Institute of Biomolecular Chemistry, National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
| | - Valentina Doneddu
- Anatomia Patologica, Azienda Ospedaliero Universitaria (AOU), 07100 Sassari, Italy.
| | - Amelia Lissia
- Anatomia Patologica, Azienda Ospedaliero Universitaria (AOU), 07100 Sassari, Italy.
| | | | - Giuseppe Palmieri
- Institute of Biomolecular Chemistry, National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
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