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Yadav M, Vaishkiar I, Sharma A, Shukla A, Mohan A, Girdhar M, Kumar A, Malik T, Mohan A. Oestrogen receptor positive breast cancer and its embedded mechanism: breast cancer resistance to conventional drugs and related therapies, a review. Open Biol 2024; 14:230272. [PMID: 38889771 DOI: 10.1098/rsob.230272] [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: 08/10/2023] [Accepted: 03/14/2024] [Indexed: 06/20/2024] Open
Abstract
Traditional medication and alternative therapies have long been used to treat breast cancer. One of the main problems with current treatments is that there is an increase in drug resistance in the cancer cells owing to genetic differences such as mutational changes, epigenetic changes and miRNA (microRNA) alterations such as miR-1246, miR-298, miR-27b and miR-33a, along with epigenetic modifications, such as Histone3 acetylation and CCCTC-Binding Factor (CTCF) hypermethylation for drug resistance in breast cancer cell lines. Certain forms of conventional drug resistance have been linked to genetic changes in genes such as ABCB1, AKT, S100A8/A9, TAGLN2 and NPM. This review aims to explore the current approaches to counter breast cancer, the action mechanism, along with novel therapeutic methods endowing potential drug resistance. The investigation of novel therapeutic approaches sheds light on the phenomenon of drug resistance including genetic variations that impact distinct forms of oestrogen receptor (ER) cancer, genetic changes, epigenetics-reported resistance and their identification in patients. Long-term effective therapy for breast cancer includes selective oestrogen receptor modulators, selective oestrogen receptor degraders and genetic variations, such as mutations in nuclear genes, epigenetic modifications and miRNA alterations in target proteins. Novel research addressing combinational therapies including maytansine, photodynamic therapy, guajadiol, talazoparib, COX2 inhibitors and miRNA 1246 inhibitors have been developed to improve patient survival rates.
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Affiliation(s)
- Manu Yadav
- Division of Genetics, ICAR- Indian Agricultural Research Institute , Pusa, New Delhi, India
| | - Ishita Vaishkiar
- Amity Institute of Biotechnology (AIB) University, Amity University Noida , Noida, India
| | - Ananya Sharma
- Department: Botany and Microbiology, Hemwati Nandan Bahuguna Garhwal University , Srinagar, India
| | - Akanksha Shukla
- School of Bioengineering and Biosciences, Lovely Professional University , Phagwara, Punjab, India
| | - Aradhana Mohan
- Department of Biomedical Engineering, University of Michigan , Ann Arbor, MI, USA
| | - Madhuri Girdhar
- Division of Research and Development, Lovely Professional University , Phagwara, Punjab, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology , New Delhi, India
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Jimma University , Jimma, Oromia 378, Ethiopia
| | - Anand Mohan
- School of Bioengineering and Biosciences, Lovely Professional University , Phagwara, Punjab, India
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King AD, Deirawan H, Klein PA, Dasgeb B, Dumur CI, Mehregan DR. Next-generation sequencing in dermatology. Front Med (Lausanne) 2023; 10:1218404. [PMID: 37841001 PMCID: PMC10570430 DOI: 10.3389/fmed.2023.1218404] [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: 05/07/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Over the past decade, Next-Generation Sequencing (NGS) has advanced our understanding, diagnosis, and management of several areas within dermatology. NGS has emerged as a powerful tool for diagnosing genetic diseases of the skin, improving upon traditional PCR-based techniques limited by significant genetic heterogeneity associated with these disorders. Epidermolysis bullosa and ichthyosis are two of the most extensively studied genetic diseases of the skin, with a well-characterized spectrum of genetic changes occurring in these conditions. NGS has also played a critical role in expanding the mutational landscape of cutaneous squamous cell carcinoma, enhancing our understanding of its molecular pathogenesis. Similarly, genetic testing has greatly benefited melanoma diagnosis and treatment, primarily due to the high prevalence of BRAF hot spot mutations and other well-characterized genetic alterations. Additionally, NGS provides a valuable tool for measuring tumor mutational burden, which can aid in management of melanoma. Lastly, NGS demonstrates promise in improving the sensitivity of diagnosing cutaneous T-cell lymphoma. This article provides a comprehensive summary of NGS applications in the diagnosis and management of genodermatoses, cutaneous squamous cell carcinoma, melanoma, and cutaneous T-cell lymphoma, highlighting the impact of NGS on the field of dermatology.
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Affiliation(s)
- Andrew D. King
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Hany Deirawan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | | | - Bahar Dasgeb
- Department of Surgical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Catherine I. Dumur
- Bernhardt Laboratories, Sonic Healthcare Anatomic Pathology Division, Jacksonville, FL, United States
| | - Darius R. Mehregan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
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Yakout NM, Abdallah DM, Abdelmonsif DA, Kholosy HM, Talaat IM, Elsakka O. BRAF V600E mutational status assessment in cutaneous melanocytic neoplasms in a group of the Egyptian population. Cancer Cell Int 2023; 23:17. [PMID: 36737739 PMCID: PMC9896695 DOI: 10.1186/s12935-023-02858-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Melanocytic neoplasms range from banal nevi to malignant melanomas. The genetic background has been extensively studied in the Caucasian population. BRAF mutations were reported among the early driver mutations in nevogenesis. Nevertheless, the pathogenesis in the Egyptian population has not been elucidated. AIM AND METHODS The present study was carried out to assess the sensitivity and specificity of immunohistochemistry (IHC) using the RM-08 clone in reference to allele-specific real-time PCR (CAST-PCR) for the detection of the BRAF V600E mutation in 50 formalin-fixed paraffin-embedded blocks of melanocytic neoplasms with prior bleaching using hydrogen peroxide in Tris-HCL and Bovine Serum Albumin respectively. RESULTS IHC staining was interpreted using staining reaction (positive versus negative) and staining pattern (negative and heterogeneous versus homogenous). Using the staining pattern, the specificity increased from 73.3 to 88.2%, the negative predictive value increased from 73.3 to 100%, the diagnostic accuracy increased from 71.4 to 90.48% and the overall accuracy increased from 69.9 to 77.3%. The sensitivity and positive predictive value remained unchanged. The K-agreement coefficient increased from 0.364 (fair agreement) to 0.741 (good agreement) and was statistically significant (p = 0.00). Next-generation sequencing was performed in 11 cases, 8 cases with IHC-positive and BRAF wild type in addition to 3 cases that failed PCR analysis and revealed no BRAF V600E. No statistically significant difference was found in the clinicopathological parameters between BRAF V600E and BRAF wild-type melanomas. CONCLUSIONS These findings suggest that IHC staining homogeneity may be more accurate in predicting BRAF V600E mutational status. However, IHC cannot replace molecular methods.
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Affiliation(s)
- Nada M. Yakout
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Dina M. Abdallah
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Doaa A. Abdelmonsif
- grid.7155.60000 0001 2260 6941Medical Biochemistry Department, Genomics Research Lab, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Hassan Mahmoud Kholosy
- grid.7155.60000 0001 2260 6941Department of Plastic Surgery, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Iman M. Talaat
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt ,grid.412789.10000 0004 4686 5317Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Omayma Elsakka
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
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Muñoz-Barrera A, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Lorenzo-Salazar JM, González-Montelongo R, García-Olivares V, Flores C. From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research. Life (Basel) 2022; 12:1939. [PMID: 36431075 PMCID: PMC9695713 DOI: 10.3390/life12111939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.
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Affiliation(s)
- Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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Dental DNA as an Indicator of Post-Mortem Interval (PMI): A Pilot Research. Int J Mol Sci 2022; 23:ijms232112896. [DOI: 10.3390/ijms232112896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Teeth have proven to be a reliable source of DNA for forensic analysis as the pulp is rich in cells and protected from damaging factors and contamination by dental hard tissues. The pilot study aims to evaluate the feasibility of Next-Generation sequencing analysis on dental pulp to detect genetic mutations in DNA caused by post-mortem cell necrosis. We used a 56-gene oncopanel kit on a sample of 17 teeth extracted from living patients. Time of the tooth avulsion was assumed as death of the individual and Post-mortem Interval (PMI) was the time elapse since the DNA extraction and analysis. Days and Accumulated Degree Days (ADD) were assumed as measures of PMI that ranged between 0 to 34 days. Only 38 of the 56 considered genes proved to be affected by mutations (101), thus being of forensic interest. More specifically, 14 mutations occurred only in a specific range of PMIs/ADD; 67 were detected (alone or as clusters of the same gene) at specific PMI/ADD; 22 occurred at every PMI/ADD, except for some specific intervals. Since dental pulp was not targeted by any oncological diseases and all teeth were intact, vital, and from patients with unremarkable medical history, it could be assumed that mutations were due to post-mortem DNA changes induced by pulp death and the increasing time elapse since death. This pilot study found encouraging results in the application of NGS analysis on dental DNA, especially for PMIs of several days for which the traditional tools for PMI estimation have limitations. Further research on a larger sample of PMI and validation research on a larger sample of PMI and validation of the results are indeed necessary.
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Catoni C, Poggiana C, Facchinetti A, Pigozzo J, Piccin L, Chiarion-Sileni V, Rosato A, Minervini G, Scaini MC. Investigating the Retained Inhibitory Effect of Cobimetinib against p.P124L Mutated MEK1: A Combined Liquid Biopsy and in Silico Approach. Cancers (Basel) 2022; 14:cancers14174153. [PMID: 36077693 PMCID: PMC9454486 DOI: 10.3390/cancers14174153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The systemic treatment of metastatic melanoma has radically changed, due to an improvement in the understanding of its genetic landscape and the advent of targeted therapy. However, the response to BRAF/MEK inhibitors is transitory, and big efforts were made to identify the mechanisms underlying the resistance. We exploited a combined approach, encompassing liquid biopsy analysis and molecular dynamics simulation, for tracking tumor evolution, and in parallel defining the best treatment option. The samples at different time points were collected from a BRAF-mutant melanoma patient who developed an early resistance to dabrafenib/trametinib. The analysis of the circulating tumor DNA (ctDNA) identified the MEK1 p.P124L mutation that confers resistance to trametinib. With an in silico modeling, we identified cobimetinib as an alternative MEK inhibitor, and consequently suggested a therapy switch to vemurafenib/cobimetinib. The patient response was followed by ctDNA tracking and circulating melanoma cell (CMC) count. The cobimetinib administration led to an important reduction in the BRAF p.V600E and MEK1 p.P124L allele fractions and in the CMC number, features suggestive of a putative response. In summary, this study emphasizes the usefulness of a liquid biopsy-based approach combined with in silico simulation, to track real-time tumor evolution while assessing the best treatment option.
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Affiliation(s)
- Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Jacopo Pigozzo
- Melanoma Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy
| | - Luisa Piccin
- Melanoma Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy
| | - Vanna Chiarion-Sileni
- Melanoma Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
- Correspondence: (A.R.); (M.C.S.)
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padua, 35121 Padua, Italy
| | - Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
- Correspondence: (A.R.); (M.C.S.)
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Laboratory diagnosis of bacterial meningitis by direct detection, serotyping and Next Generation Sequencing: How 10 years of testing in New York State has evolved to improve laboratory diagnosis and public health. Mol Cell Probes 2021; 61:101786. [PMID: 34863914 DOI: 10.1016/j.mcp.2021.101786] [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: 09/17/2021] [Revised: 11/09/2021] [Accepted: 11/27/2021] [Indexed: 11/23/2022]
Abstract
Since 2005, the Wadsworth Center (WC) has provided molecular testing on cerebrospinal fluid (CSF) and whole blood specimens in close collaboration with epidemiologists in New York State and New York City. In this study, we analyzed 10 years of data to demonstrate the significant value of utilizing molecular methods to assess patient specimens for etiologic agents of bacterial meningitis. A comprehensive molecular testing algorithm to detect and serotype/serogroup bacterial agents known to cause bacterial meningitis (Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus agalactiae) has evolved, and retrospective specimen testing has been essential for each improvement. Over a ten-year span from 2010 to 2019 the WC received 831 specimens from 634 patients with suspected bacterial meningitis. Real-time PCR was positive for at least one of the agents in 223 (27%) specimens from 183 patients (29%). Of the 223 positives, 146 (66%) were further characterized by real-time PCR into serogroup/serotype. Additionally, examination of 131 paired specimens of CSF and whole blood from the same patients found better detection in CSF, but whole blood is a useful alternative for diagnosis when CSF is not available. For specimens initially PCR-negative, 16S rDNA Sanger sequencing was requested by the submitter for 146 cases resulting in the identification of bacterial agents in an additional 24 (16%) specimens. In a retrospective study, Next Generation Sequencing (NGS) was evaluated for the detection of pathogens in 53 previously tested PCR-negative CSF specimens and identified bacteria in 14 (26%) specimens. This molecular testing algorithm has provided clinicians a diagnosis when culture is negative with the potential to guide therapy. It has also aided public health in determining when antibiotic prophylaxis was needed, augmented surveillance data to yield a fuller picture of community prevalence, and highlighted gaps in the spectrum of agents that cause bacterial meningitis.
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Luo S, Raval V, Zabor EC, Singh AD. Small Choroidal Melanoma: Correlation between Clinical Characteristics and Metastatic Potential. Ocul Oncol Pathol 2021; 7:437-446. [PMID: 35087820 PMCID: PMC8740206 DOI: 10.1159/000519672] [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: 05/13/2021] [Accepted: 09/10/2021] [Indexed: 11/19/2022] Open
Abstract
IMPORTANCE Diagnosis of small choroidal melanoma is based upon clinical features and presence of factors predictive of local malignant growth. Prognostic biopsy quantifies risk of metastasis. OBJECTIVE The aim of this study is to explore relationship between clinical characteristics and metastatic potential of a small choroidal melanoma. DESIGN Retrospective review of 53 patients with small choroidal melanoma treated in a tertiary oncology clinic. Patients were derived from 3 cohorts, with pathologic confirmation, with growth confirmation, and those treated only on clinical basis. Based upon prognostic biopsy outcomes, each case was classified into low or high metastatic potential groups. Distribution of clinical characteristics such as age, laterality, symptoms, tumor dimensions, tumor distance from optic nerve and fovea, presence of surface orange pigment, drusen, retinal pigment epithelial atrophy, and subretinal fluid was analyzed between metastatic groups. MAIN OUTCOME MEASURES Distribution of clinical characteristics between low or high metastatic potential groups was analyzed. RESULTS A total of 53 patients [mean age, 61 years (range, 27-81 years); 32 (60%) men and 21 (40%) women] were classified into pathology confirmed group (n = 13), growth confirmed group (n = 26), and with clinical group (n = 14). Prognostic biopsy in the growth, pathology, and clinical groups revealed low metastatic potential in 23, 10, and 11 patients, respectively, and high metastatic potential in 3 patients in each group. Distribution of clinical characteristics between low or high metastatic potential groups was not statistically significantly different. CONCLUSION Clinical characteristics do not identify metastatic potential of a small choroidal melanoma.
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Affiliation(s)
- Shiming Luo
- Department of Quantitative Health Sciences & Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Vishal Raval
- Department of Quantitative Health Sciences & Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Emily C Zabor
- Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Arun D Singh
- Department of Quantitative Health Sciences & Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
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Abstract
Importance The extent to which uveal melanoma is cured by ocular therapy is not known. Objective To estimate cured fractions (CF) of uveal melanoma using combination of institutional and Surveillance, Epidemiology, and End Results (SEER) data. Design, Setting, and Participants Integrative analysis of 42 years of SEER data (1975-2016) with 25 years (1993-2018) of complementary institutional data. The analysis included SEER US patients and molecularly prognosticated patients in the United States and Europe. Three SEER databases (SEER-9, SEER-13, and SEER-18) were merged. A total of 10 678 SEER cases of uveal melanoma diagnosed from 1975 to 2016 using International Classification of Disease for Oncology morphology codes 8720-8790 (for melanoma) and site codes C69.2-4 (for choroid, ciliary body, and iris) were downloaded April 16, 2019. The institutional data included 5 institutional cohorts of 788 molecularly prognosticated patients (diagnosed prior to July 2019) with 3115 person-years at risk of death and 262 observed deaths. Main Outcomes and Measures Excess absolute risks of death (EAR) and cured fraction (CF) indicates lifetime area under the EAR curve. These are applied to populations and subpopulations. Results The SEER EAR, with sexes and races pooled, can be modeled as a sum of 2 waves. The first wave peaks at approximately 3 years and is negligible by 15 years, at which time the second wave peaks. Institutional data suggest that the first wave is owing to BAP1 mutant cases (204 of 355 [57.5%]; 95% CI, 52%-63%) and that the second wave is owing to BAP1 wild-type SF3B1 mutant cases (60 of 355 [17%]; 95% CI, 13%-21%). There is also a third group with a low flat EAR time course (91 of 355 [25.5%]; 95% CI, 21%-30%). The overall statistical CF of 60% is reached by approximately 25 years. Conclusions and Relevance These findings suggest that the benefits of ocular therapy for curing uveal melanoma may be questionable because statistical cures reflect deaths of poor prognosis cases and survival of good prognosis cases. Changes in uveal melanoma patient management may be needed to improve survival.
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Affiliation(s)
- Arun D Singh
- Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | - Emily C Zabor
- Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Tomas Radivoyevitch
- Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
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Grzywa TM, Koppolu AA, Paskal W, Klicka K, Rydzanicz M, Wejman J, Płoski R, Włodarski PK. Higher Mutation Burden in High Proliferation Compartments of Heterogeneous Melanoma Tumors. Int J Mol Sci 2021; 22:3886. [PMID: 33918692 PMCID: PMC8069012 DOI: 10.3390/ijms22083886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
Melanoma tumors are the most heterogeneous of all tumor types. Tumor heterogeneity results in difficulties in diagnosis and is a frequent cause of failure in treatment. Novel techniques enable accurate examination of the tumor cells, considering their heterogeneity. The study aimed to determine the somatic variations among high and low proliferating compartments of melanoma tumors. In this study, 12 archival formalin-fixed paraffin-embedded samples of previously untreated primary cutaneous melanoma were stained with Ki-67 antibody. High and low proliferating compartments from four melanoma tumors were dissected using laser-capture microdissection. DNA was isolated and analyzed quantitatively and qualitatively. Libraries for amplicon-based next-generation sequencing (NGS) were prepared using NEBNext Direct Cancer HotSpot Panel. NGS detected 206 variants in 42 genes in melanoma samples. Most of them were located within exons (135, 66%) and were predominantly non-synonymous single nucleotide variants (99, 73.3%). The analysis showed significant differences in mutational profiles between high and low proliferation compartments of melanoma tumors. Moreover, a significantly higher percentage of variants were detected only in high proliferation compartments (39%) compared to low proliferation regions (16%, p < 0.05). Our results suggest a significant functional role of genetic heterogeneity in melanoma.
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Affiliation(s)
- Tomasz M. Grzywa
- Center for Preclinical Research, The Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-097 Warsaw, Poland; (T.M.G.); (W.P.); (K.K.)
- Doctoral School, Medical University of Warsaw, 61 Zwirki and Wigury Str., 02-091 Warsaw, Poland
- Department of Immunology, Medical University of Warsaw, 5 Nielubowicza Str., 02-097 Warsaw, Poland
| | - Agnieszka A. Koppolu
- Department of Medical Genetics, Medical University of Warsaw, 3C Pawinskiego Str., 02-106 Warsaw, Poland; (A.A.K.); (M.R.); (R.P.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Wiktor Paskal
- Center for Preclinical Research, The Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-097 Warsaw, Poland; (T.M.G.); (W.P.); (K.K.)
| | - Klaudia Klicka
- Center for Preclinical Research, The Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-097 Warsaw, Poland; (T.M.G.); (W.P.); (K.K.)
- Doctoral School, Medical University of Warsaw, 61 Zwirki and Wigury Str., 02-091 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 3C Pawinskiego Str., 02-106 Warsaw, Poland; (A.A.K.); (M.R.); (R.P.)
| | - Jarosław Wejman
- Department of Pathology, Medical Center of Postgraduate Education, 00-416 Warsaw, Poland;
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 3C Pawinskiego Str., 02-106 Warsaw, Poland; (A.A.K.); (M.R.); (R.P.)
| | - Paweł K. Włodarski
- Center for Preclinical Research, The Department of Methodology, Medical University of Warsaw, 1B Banacha Str., 02-097 Warsaw, Poland; (T.M.G.); (W.P.); (K.K.)
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Mokánszki A, Méhes G, Csoma SL, Kollár S, Chang Chien YC. Molecular Profiling of Merkel Cell Polyomavirus-Associated Merkel Cell Carcinoma and Cutaneous Melanoma. Diagnostics (Basel) 2021; 11:diagnostics11020212. [PMID: 33535453 PMCID: PMC7912722 DOI: 10.3390/diagnostics11020212] [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: 12/22/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023] Open
Abstract
Merkel cell carcinoma (MCC) is a rare, high-grade, aggressive cutaneous neuroendocrine malignancy most commonly associated with sun-exposed areas of older individuals. A relatively newly identified human virus, the Merkel cell polyomavirus (MCPyV) has been implicated in the pathogenesis of MCC. Our study aimed to examine nine MCC cases and randomly selected 60 melanoma cases to identify MCPyV status and to elucidate genetic differences between virus-positive and -negative cases. Altogether, seven MCPyV-positive MCC samples and four melanoma samples were analyzed. In MCPyV-positive MCC RB1, TP53, FBXW7, CTNNB1, and HNF1A pathogenic variants were identified, while in virus-negative cases only benign variants were found. In MCPyV-positive melanoma cases, besides BRAF mutations the following genes were also affected: PIK3CA, STK11, CDKN2A, SMAD4, and APC. In contrast to studies found in the literature, a higher tumor burden was detected in virus-associated MCC compared to MCPyV-negative cases. No association was identified between virus infection and tumor burden in melanoma samples. We concluded that analyzing the key morphologic and immunohistological features of MCC is critical to avoid confusion with other cutaneous malignancies. Molecular genetic investigations such as next-generation sequencing (NGS) enable molecular stratification, which may have future clinical impact.
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Affiliation(s)
- Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (G.M.); (S.L.C.); (Y.-C.C.C.)
- Correspondence: ; Tel.: +36-52-411-600
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (G.M.); (S.L.C.); (Y.-C.C.C.)
| | - Szilvia Lilla Csoma
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (G.M.); (S.L.C.); (Y.-C.C.C.)
| | - Sándor Kollár
- Department of Pathology, Kenézy Gyula Teaching Hospital, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Yi-Che Chang Chien
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (G.M.); (S.L.C.); (Y.-C.C.C.)
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12
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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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13
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Vanni I, Tanda ET, Spagnolo F, Andreotti V, Bruno W, Ghiorzo P. The Current State of Molecular Testing in the BRAF-Mutated Melanoma Landscape. Front Mol Biosci 2020; 7:113. [PMID: 32695793 PMCID: PMC7338720 DOI: 10.3389/fmolb.2020.00113] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/13/2020] [Indexed: 01/19/2023] Open
Abstract
The incidence of melanoma, among the most lethal cancers, is widespread and increasing. Metastatic melanoma has a poor prognosis, representing about 90% of skin cancer mortality. The increased knowledge of tumor biology and the greater understanding of the immune system role in the anti-tumor response has allowed us to develop a more rational approach to systemic therapies. The discovery of activating BRAF mutations in half of all melanomas has led to the development of molecularly targeted therapy with BRAF and MEK inhibitors, which dramatically improved outcomes of patients with stage IV BRAF-mutant melanoma. More recently, the results of clinical phase III studies conducted in the adjuvant setting led to the combined administration of BRAF and MEK inhibitors also in patients with resected high-risk melanoma (stage III). Therefore, BRAF mutation testing has become a priority to determine the oncologist's choice and course of therapy. In this review, we will report the molecular biology-based strategies used for BRAF mutation detection with the main advantages and disadvantages of the most commonly used diagnostic strategies. The timing of such molecular assessment in patients with cutaneous melanoma will be discussed, and we will also examine considerations and approaches for accurate and effective BRAF testing.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 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, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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14
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Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma. Cancers (Basel) 2020; 12:cancers12041039. [PMID: 32340176 PMCID: PMC7226611 DOI: 10.3390/cancers12041039] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
Uveal melanoma (UM) has well-characterised somatic copy number alterations (SCNA) in chromosomes 1, 3, 6 and 8, in addition to mutations in GNAQ, GNA11, CYSLTR2, PLCB4, BAP1, SF3B1 and EIF1AX, most being linked to metastatic-risk. To gain further insight into the molecular landscape of UM, we designed a targeted next-generation sequencing (NGS) panel to detect SCNA and mutations in routine clinical UM samples. We compared hybrid-capture and amplicon-based target enrichment methods and tested a larger cohort of primary UM samples on the best performing panel. UM clinical samples processed either as fresh-frozen, formalin-fixed paraffin embedded (FFPE), small intraocular biopsies or following irradiation were successfully profiled using NGS, with hybrid capture outperforming the PCR-based enrichment methodology. We identified monosomy 3 (M3)-UM that were wild-type for BAP1 but harbored SF3B1 mutations, novel frameshift deletions in SF3B1 and EIF1AX, as well as a PLCB4 mutation outside of the hotspot on exon 20 coinciding with a GNAQ mutation in some UM. We observed samples that harboured mutations in both BAP1 and SF3B1, and SF3B1 and EIF1AX, respectively. Novel mutations were also identified in TTC28, KTN1, CSMD1 and TP53BP1. NGS can simultaneously assess SCNA and mutation data in UM, in a reliable and reproducible way, irrespective of sample type or previous processing. BAP1 and SF3B1 mutations, in addition to 8q copy number, are of added importance when determining UM patient outcome.
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15
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Steeghs EMP, Kroeze LI, Tops BBJ, van Kempen LC, Ter Elst A, Kastner-van Raaij AWM, Hendriks-Cornelissen SJB, Hermsen MJW, Jansen EAM, Nederlof PM, Schuuring E, Ligtenberg MJL, Eijkelenboom A. Comprehensive routine diagnostic screening to identify predictive mutations, gene amplifications, and microsatellite instability in FFPE tumor material. BMC Cancer 2020; 20:291. [PMID: 32264863 PMCID: PMC7137451 DOI: 10.1186/s12885-020-06785-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/25/2020] [Indexed: 02/08/2023] Open
Abstract
Background Sensitive and reliable molecular diagnostics is needed to guide therapeutic decisions for cancer patients. Although less material becomes available for testing, genetic markers are rapidly expanding. Simultaneous detection of predictive markers, including mutations, gene amplifications and MSI, will save valuable material, time and costs. Methods Using a single-molecule molecular inversion probe (smMIP)-based targeted next-generation sequencing (NGS) approach, we developed an NGS panel allowing detection of predictive mutations in 33 genes, gene amplifications of 13 genes and microsatellite instability (MSI) by the evaluation of 55 microsatellite markers. The panel was designed to target all clinically relevant single and multiple nucleotide mutations in routinely available lung cancer, colorectal cancer, melanoma, and gastro-intestinal stromal tumor samples, but is useful for a broader set of tumor types. Results The smMIP-based NGS panel was successfully validated and cut-off values were established for reliable gene amplification analysis (i.e. relative coverage ≥3) and MSI detection (≥30% unstable loci). After validation, 728 routine diagnostic tumor samples including a broad range of tumor types were sequenced with sufficient sensitivity (2.4% drop-out), including samples with low DNA input (< 10 ng; 88% successful), low tumor purity (5–10%; 77% successful), and cytological material (90% successful). 75% of these tumor samples showed ≥1 (likely) pathogenic mutation, including targetable mutations (e.g. EGFR, BRAF, MET, ERBB2, KIT, PDGFRA). Amplifications were observed in 5.5% of the samples, comprising clinically relevant amplifications (e.g. MET, ERBB2, FGFR1). 1.5% of the tumor samples were classified as MSI-high, including both MSI-prone and non-MSI-prone tumors. Conclusions We developed a comprehensive workflow for predictive analysis of diagnostic tumor samples. The smMIP-based NGS analysis was shown suitable for limited amounts of histological and cytological material. As smMIP technology allows easy adaptation of panels, this approach can comply with the rapidly expanding molecular markers.
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Affiliation(s)
- Elisabeth M P Steeghs
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Bastiaan B J Tops
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.,Department of Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Leon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arja Ter Elst
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | - Mandy J W Hermsen
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.
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16
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Castillo P, Marginet M, Jares P, García M, Gonzalvo E, Arance A, García A, Alos L, Teixido C. Implementation of an NGS panel for clinical practice in paraffin-embedded tissue samples from locally advanced and metastatic melanoma patients. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:101-108. [PMID: 36046072 PMCID: PMC9400780 DOI: 10.37349/etat.2020.00006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/12/2020] [Indexed: 12/22/2022] Open
Abstract
Aim: Single biomarker diagnostic test of BRAFV600 locus in metastatic melanoma is mandatory for treatment decision; however, multiple-gene based techniques, such as targeted next-generation sequencing (NGS) are being used to maximize the number of patients that can benefit from a targeted therapy. The main objective of this study is to investigate whether an NGS panel could be adopted in routine clinical care for advanced melanoma. Methods: Patients diagnosed with advanced melanoma at our center from 2017 to 2019 were included. Presence of genetic alterations was performed using two methods: real-time polymerase chain reaction-based Idylla test (Biocartis) and NGS with the oncomine solid tumor DNA kit (Thermo Fisher Scientific). Total genomic DNA was extracted from formalin-fixed and paraffin embedded samples for sequencing. Results: A total of 155 samples were evaluated for molecular analysis but 40 samples (25.8%) were inadequate for sequencing. The clinical utility of BRAFV600 real-time polymerase chain reaction and targeted-NGS was compared in 29 samples and a very good concordance was observed (Kappa = 0.89, 95% confidence interval 0.68 ± 1.05). An oncogenic mutation by NGS was found in 75 samples (65%)–53% of whom were candidates for personalized therapies. The most prevalent mutated genes were BRAF (39%), TP53 (23%), and NRAS (14%). Other genes identified at lower incidence (< 5%) were: PIK3CA, ERBB4, CTNNB1, STK11, FGFR1, SMAD4, KRAS, FGFR3, PTEN and AKT. Co-occurrence of oncogenic mutations was detected in 40% of the samples. Among the mutations identified, TP53 was significantly more prevalent in men (men 31.8% versus women 12.2%, P = 0.03) and NRAS in women (men 9.1% versus women 24.4%, P = 0.03). Conclusions: Targeted-NGS testing is a feasible technique to implement in the routine clinical practice. Based on our results, NGS has provided more information on target-genes than RT-PCR technique, maximizing the benefit for patients with advanced melanoma.
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Affiliation(s)
- Paola Castillo
- Department of Pathology, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Marta Marginet
- Department of Pathology, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Pedro Jares
- Department of Pathology, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Mireia García
- Department of Pathology, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Elena Gonzalvo
- Department of Pathology, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Ana Arance
- Department of Medical Oncology, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Adriana García
- Department of Pathology, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Llucia Alos
- Department of Pathology, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Cristina Teixido
- Department of Pathology, Hospital Clinic, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
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17
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Association of epigenetics of the PDK4 gene in skeletal muscle and peripheral blood with exercise therapy following artificial knee arthroplasty. J Physiol Anthropol 2020; 39:7. [PMID: 32216839 PMCID: PMC7098095 DOI: 10.1186/s40101-020-00216-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/10/2020] [Indexed: 12/22/2022] Open
Abstract
Background Although exercise is a standard treatment for postoperative osteoarthritis, interindividual differences have been reported. Epigenetic modification (DNA methylation), a factor causing interindividual differences, is altered by the environment and may affect all tissues. Performing a tissue biopsy to investigate methylation of skeletal muscle fat metabolism genes is invasive, and less invasive and convenient alternatives such as blood testing are desired. However, the relationship between tissue and blood is still unclear. Here, we examined the relationship between DNA methylation of the PDK4 gene in skeletal muscle and peripheral blood. Patients and methods Five patients who underwent artificial knee arthroplasty between April 2017 and June 2018 at Kansai Medical University Hospital were included (2 men and 3 women; average age, 75.2 years; body mass index, 26.1 kg/m2). We measured the body composition of the patients using dual-energy X-ray absorptiometry. Peripheral blood was collected at the time of hospitalization and 5 months after surgery; skeletal muscles were collected at the time of surgery and 5 months after surgery. Rehabilitation was performed according to the clinical procedure for 3 months after surgery. Patients performed resistance training and aerobic exercise using an ergometer for 20 min twice a week. Biopsy samples were treated with bisulfite after DNA extraction, and the methylation rate was calculated at different CpG islands downstream from the transcription initiation codon of the PDK4 gene. Results No significant change in body composition was observed before and after postoperative exercise therapy, and no significant change was noted in the methylation at each position in the promoter region of PDK4 in the skeletal muscle and peripheral blood. However, changes in the methylation rate at CpG1 in peripheral blood significantly correlated with those in skeletal muscle (P = 0.037). Furthermore, the amount of change in the methylation rate of CpG1 in the skeletal muscle was significantly correlated (P = 0.037) with the average methylation rate at the promoter region in peripheral blood. Conclusions Methylation rates at CpG1 in the skeletal muscle and peripheral blood were significantly correlated, suggesting that skeletal muscle methylation could be analyzed via peripheral blood rather than skeletal muscle biopsy.
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18
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In Situ Profiling of the Three Dominant Phyla Within the Human Gut Using TaqMan PCR for Pre-Hospital Diagnosis of Gut Dysbiosis. Int J Mol Sci 2020; 21:ijms21061916. [PMID: 32168885 PMCID: PMC7139488 DOI: 10.3390/ijms21061916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 12/26/2022] Open
Abstract
A microbial imbalance called dysbiosis leads to inflammatory bowel disease (IBD), which can include ulcerative colitis (UC). Fecal microbiota transplantation (FMT), a novel therapy, has recently been successful in treating gut dysbiosis in UC patients. For the FMT technique to be successful, the gut microbiota of both the healthy donors and UC patients must be characterized. For decades, next-generation sequencing (NGS) has been used to analyze gut microbiota. Despite the popularity of NGS, the cost and time constraints make it difficult to use in emergency services and activities related to the periodic monitoring of microbiota profile alterations. Hence, in this study, we developed a multiplex TaqMan qPCR assay (MTq-PCR) with novel probes to simultaneously determine the relative proportions of the three dominant microbial phyla in the human gut: Bacteroidetes, Firmicutes, and Proteobacteria. The relative proportions of the three phyla in fecal samples of either healthy volunteers or UC patients were similar when assessed NGS and the MTq-PCR. Thus, our MTq-PCR assay could be a practical microbiota profiling alternative for diagnosing and monitoring gut dysbiosis in UC patients during emergency situations, and it could have a role in screening stool from potential FMT donors.
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19
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Olbryt M, Pigłowski W, Rajczykowski M, Pfeifer A, Student S, Fiszer-Kierzkowska A. Genetic Profiling of Advanced Melanoma: Candidate Mutations for Predicting Sensitivity and Resistance to Targeted Therapy. Target Oncol 2020; 15:101-113. [PMID: 31980996 PMCID: PMC7028806 DOI: 10.1007/s11523-020-00695-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Molecularly targeted therapy has revolutionized the treatment of advanced melanoma. However, despite its high efficiency, a majority of patients experience relapse within 1 year of treatment because of acquired resistance, and approximately 10-25% patients gain no benefit from these agents owing to intrinsic resistance. This is mainly caused by the genetic heterogeneity of melanoma cells. OBJECTIVE We aimed to validate the predictive significance of selected genes in advanced melanoma patients before treatment with BRAF/MEK inhibitors. PATIENTS AND METHODS Archival DNA derived from 37 formalin-fixed paraffin-embedded pre-treatment advanced melanoma samples of patients treated with targeted therapy was used for next-generation sequencing analysis using the Ion Torrent platform. The AmpliSeq Custom Panel comprised coding sequences or hot spots of 23 melanoma genes: ATM, BRAF, CDK4, CDKN2A, CTNNB1, EGFR, HOXD8, HRAS, IDH1, KIT, KRAS, MAP3K8, MAP2K1, MAP2K2, MITF, MYC, NF1, NRAS, PAX5, PIK3R1, PTEN, RAC1, and RB1. The sequences were evaluated for genomic alterations and further validated using Sanger sequencing. RESULTS Our analysis revealed non-BRAF genetic alterations in 28 out of 37 samples (75.7%). Genetic changes were identified in PTEN, CDK4, CDKN2A, CTNNB1, EGFR, HOXD8, HRAS, KIT, MAP2K1, MAP2K2, MITF, MYC, NF1, PAX5, RAC1, and RB1. Fifteen known pathogenic mutations (single nucleotide variants or indels) and 11 variants of unknown significance were detected. Statistical analysis revealed an association between the presence of pathogenic mutations and time to progression during treatment with combination therapy. CONCLUSIONS Pathogenic mutations identified by gene panel sequencing have potential predictive value for targeted therapy of melanoma and are worth further validation in a larger series of cases. The role of some known mutations (e.g. CDK4R24, PTEN c.801 + 1G > A, CTNNB1S45F) as well as variants of unknown significance identified in this study (e.g. MITFR316K, KITG498S) in the generation of resistance to BRAF/MEK inhibitors should be further investigated.
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Affiliation(s)
- Magdalena Olbryt
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Wybrzeze Armii Krajowej 15, Gliwice, Poland.
| | - Wojciech Pigłowski
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Wybrzeze Armii Krajowej 15, Gliwice, Poland
- Tumor Pathology Department, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Gliwice, Poland
| | - Marcin Rajczykowski
- II Clinic of Radiotherapy and Chemotherapy, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Gliwice, Poland
| | - Aleksandra Pfeifer
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Gliwice, Poland
| | - Sebastian Student
- Department of Systems Biology and Engineering, Silesian University of Technology, Akademicka 16, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, Gliwice, Poland
| | - Anna Fiszer-Kierzkowska
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Wybrzeze Armii Krajowej 15, Gliwice, Poland
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20
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Park C, Kim M, Kim MJ, Kim H, Ock CY, Keam B, Kim TM, Kim DW, Kim JI, Heo DS. Clinical Application of Next-Generation Sequencing-Based Panel to BRAF Wild-Type Advanced Melanoma Identifies Key Oncogenic Alterations and Therapeutic Strategies. Mol Cancer Ther 2019; 19:937-944. [PMID: 31826932 DOI: 10.1158/1535-7163.mct-19-0457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 08/12/2019] [Accepted: 12/06/2019] [Indexed: 11/16/2022]
Abstract
Molecular profiling with next-generation sequencing (NGS) has been applied in multiple solid cancers to discover potential therapeutic targets. Here, we describe the results of a clinical NGS panel in patients with advanced melanoma. Thirty-six tumor tissues from patients with BRAF wild-type melanoma at Seoul National University Hospital (SNUH; Seoul, Republic of Korea) were collected and deep-sequenced using the SNUH FIRST-Cancer NGS panel to assess single-nucleotide variants, small insertions/deletions, copy number variations, and structural variations to estimate tumor mutation burden (TMB). We discovered 106 oncogenic alterations and most of the patients (n = 33, 92%) harbored at least one oncogenic alteration, including 2 patients who were initially diagnosed as BRAF V600E-negative but were later confirmed to be positive. Altogether, 36 samples were classified into RAS/BRAF/NF1-mutant (n = 14, 39%) or triple wild-type (n = 22, 61%) melanoma subtypes. The estimated median TMB was 8.2 mutations per Mb, ranging from 0 to 146.67 mutations per Mb. Of the 36 patients, 25 (70%) had actionable alterations with currently developed drugs, and 7 (19.4%) were enrolled in clinical trials with an RAF inhibitor, multiple receptor tyrosine kinase inhibitor, and anti-programmed cell death-1 (PD-1) antibody. TMB tended to associate with progression-free survival (PFS) of treatment with anti-PD-1/PDL-1 antibody (HR, 0.96; 95% confidence interval, 0.92-1.00; P = 0.07). High-TMB (≥13) group was associated with longer PFS than the low-TMB group (median 34.0 vs. 11.0 weeks, P = 0.04). Overall, the clinical use of a NGS panel in patients with advanced melanoma shows association with clinical outcomes and several therapeutic strategies.
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Affiliation(s)
- Changhee Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea. .,Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Min Jung Kim
- Genome Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea.
| | - Hyeongmin Kim
- Genome Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Chan-Young Ock
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.,Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Bhumsuk Keam
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.,Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Tae Min Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.,Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Dong-Wan Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.,Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Jong-Il Kim
- Genome Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Dae Seog Heo
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.,Seoul National University Cancer Research Institute, Seoul, Republic of Korea
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21
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Zhang QG, Wang J, Gong WY, Jing QC. Clonal evolution in a chronic neutrophilic leukemia patient. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2019; 24:455-458. [PMID: 31076019 DOI: 10.1080/16078454.2019.1613291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objectives and importance: Chronic neutrophilic leukemia (CNL) is a distinct myeloproliferative neoplasm with a high prevalence (>80%) of mutations in the colony-stimulating factor 3 receptor (CSF3R); these mutations activate the receptor, leading to the proliferation of neutrophils that are a hallmark of CNL. Clinical presentation: We present a male patient who presented peripheral blood leukocytosis. On the basis of his morphological appearances and molecular findings he was determined to have a diagnosis of chronic neutrophilic leukemia. At a follow-up at 7 months, in addition to the CSF3R c.2373G > A (p.W791*) truncated mutation, another CSF3R mutation appeared as c.1853C > T(p.T618I). Discussion and conclusion: We present the first patient with a diagnosis of chronic neutrophilic leukemia with a c.2373G > A (p.W791*) truncated mutation of CSF3R. These findings elucidate a novel paradigm of CNL pathogenesis and explain how mutations drive the development of the disease. The order of acquisition of CSF3R mutations relative to mutations in epigenetic modifiers and the spliceosome have been determined only in isolated case reports; thus, further work is needed to understand the impact of mutation chronology on the clonal evolution and progression of CNL.
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Affiliation(s)
- Qi-Guo Zhang
- a Department of Hematology , The First People's Hospital of Chuzhou City , Chuzhou , People's Republic of China.,b Chuzhou Clinical College of Anhui Medical University , Chuzhou , People's Republic of China.,c Department of Hematology , the Affiliated Drum Tower Hospital of Nanjing University Medical School , Nanjing , People's Republic of China
| | - Jing Wang
- c Department of Hematology , the Affiliated Drum Tower Hospital of Nanjing University Medical School , Nanjing , People's Republic of China
| | - Wen-Yu Gong
- a Department of Hematology , The First People's Hospital of Chuzhou City , Chuzhou , People's Republic of China.,b Chuzhou Clinical College of Anhui Medical University , Chuzhou , People's Republic of China
| | - Qi-Chuan Jing
- a Department of Hematology , The First People's Hospital of Chuzhou City , Chuzhou , People's Republic of China.,b Chuzhou Clinical College of Anhui Medical University , Chuzhou , People's Republic of China
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Analytical Evaluation of an NGS Testing Method for Routine Molecular Diagnostics on Melanoma Formalin-Fixed, Paraffin-Embedded Tumor-Derived DNA. Diagnostics (Basel) 2019; 9:diagnostics9030117. [PMID: 31547467 PMCID: PMC6787639 DOI: 10.3390/diagnostics9030117] [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: 08/05/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Next Generation Sequencing (NGS) is a promising tool for the improvement of tumor molecular profiling in view of the identification of a personalized treatment in oncologic patients. To verify the potentiality of a targeted NGS (Ion AmpliSeq™ Cancer Hotspot Panel v2), selected melanoma samples (n = 21) were retrospectively analyzed on S5 platform in order to compare NGS performance with the conventional techniques adopted in our routine clinical setting (Sequenom MassARRAY system, Sanger sequencing, allele-specific real-time PCR). The capability in the identification of rare and low-frequency mutations in the main genes involved in melanoma (BRAF and NRAS genes) was verified and integrated with the results deriving from other oncogenes and tumor suppressor genes. The analytical evaluation was carried out by the analysis of DNA derived from control cell lines and FFPE (Formalin-Fixed, Paraffin-Embedded) samples to verify that the achieved resolution of uncommon mutations and low-frequency variants was suitable to meet the technical and clinical requests. Our results demonstrate that the amplicon-based NGS approach can reach the sensitivity proper of the allele-specific assays together with the high specificity of a sequencing method. An overall concordance among the tested methods was observed in the identification of classical and uncommon mutations. The assessment of the quality parameters and the comparison with the orthogonal methods suggest that the NGS method could be implemented in the clinical setting for melanoma molecular characterization.
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23
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Manca A, Paliogiannis P, Colombino M, Casula M, Lissia A, Botti G, Caracò C, Ascierto PA, Sini MC, Palomba G, Pisano M, Doneddu V, Cossu A, Palmieri G. Mutational concordance between primary and metastatic melanoma: a next-generation sequencing approach. J Transl Med 2019; 17:289. [PMID: 31455347 PMCID: PMC6712827 DOI: 10.1186/s12967-019-2039-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 08/18/2019] [Indexed: 12/21/2022] Open
Abstract
Background Cutaneous malignant melanoma (CMM) is one of the most common skin cancers worldwide. Limited information is available in the current scientific literature on the concordance of genetic alterations between primary and metastatic CMM. In the present study, we performed next-generation sequencing (NGS) analysis of the main genes participating in melanoma pathogenesis and progression, among paired primary and metastatic lesions of CMM patients, with the aim to evaluate levels of discrepancies in mutational patterns. Methods Paraffin-embedded tumor tissues of the paired lesions were retrieved from the archives of the institutions participating in the study. NGS was performed using a specific multiple-gene panel constructed by the Italian Melanoma Intergroup (IMI) to explore the mutational status of selected regions (343 amplicons; amplicon range: 125–175 bp; coverage 100%) within the main 25 genes involved in CMM pathogenesis; sequencing was performed with the Ion Torrent PGM System. Results A discovery cohort encompassing 30 cases, and a validation cohort including eleven Sardinian patients with tissue availability from both the primary and metachronous metastatic lesions were identified; the global number of analyzed tissue specimens was 90. A total of 829 genetic non-synonymous variants were detected: 101 (12.2%) were pathogenic/likely pathogenic, 131 (15.8%) were benign/likely benign, and the remaining 597 (72%) were uncertain/unknown significance variants. Considering the global cohort, the consistency in pathogenic/pathogenic like mutations was 76%. Consistency for BRAF and NRAS mutations was 95.2% and 85.7% respectively, without statistically significant differences between the discovery and validation cohort. Conclusions Our study showed a high level of concordance in mutational patterns between primary and metastatic CMM, especially when pathogenic mutations in driver genes were considered.
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Affiliation(s)
- Antonella Manca
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry, National Research Council, Traversa La Crucca 3, 07100, Sassari, Italy
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Viale San Pietro 43, 07100, Sassari, Italy
| | - Maria Colombino
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry, National Research Council, Traversa La Crucca 3, 07100, Sassari, Italy
| | - Milena Casula
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry, National Research Council, Traversa La Crucca 3, 07100, Sassari, Italy
| | - Amelia Lissia
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Viale San Pietro 43, 07100, Sassari, Italy
| | - Gerardo Botti
- Istituto Nazionale Tumori "Fondazione Pascale", Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Corrado Caracò
- Istituto Nazionale Tumori "Fondazione Pascale", Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Paolo A Ascierto
- Istituto Nazionale Tumori "Fondazione Pascale", Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Maria Cristina Sini
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry, National Research Council, Traversa La Crucca 3, 07100, Sassari, Italy
| | - Grazia Palomba
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry, National Research Council, Traversa La Crucca 3, 07100, Sassari, Italy
| | - Marina Pisano
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry, National Research Council, Traversa La Crucca 3, 07100, Sassari, Italy
| | | | | | - Valentina Doneddu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Viale San Pietro 43, 07100, Sassari, Italy
| | - Antonio Cossu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Viale San Pietro 43, 07100, Sassari, Italy
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry, National Research Council, Traversa La Crucca 3, 07100, Sassari, Italy.
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24
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Lokhandwala PM, Tseng LH, Rodriguez E, Zheng G, Pallavajjalla A, Gocke CD, Eshleman JR, Lin MT. Clinical mutational profiling and categorization of BRAF mutations in melanomas using next generation sequencing. BMC Cancer 2019; 19:665. [PMID: 31277584 PMCID: PMC6612071 DOI: 10.1186/s12885-019-5864-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/20/2019] [Indexed: 12/18/2022] Open
Abstract
Background Analysis of melanomas for actionable mutations has become the standard of care. Recently, a classification scheme has been proposed that categorizes BRAF mutations based on their mechanisms for activation of the MAPK pathway. Methods In this analysis BRAF, KIT, NRAS, and PIK3CA mutations were examined by next generation sequencing (NGS) in 446 melanomas in a clinical diagnostic setting. KRAS and HRAS were also analyzed to elucidate coexisting BRAF and RAS mutations. BRAF mutations were categorized into class-1 (kinase-activated, codon 600), class-2 (kinase-activated, non-codon 600) and class-3 (kinase-impaired), based on the newly proposed classification scheme. Results NGS demonstrated high analytic sensitivity. Among 355 mutations detected, variant allele frequencies were 2–5% in 21 (5.9%) mutations and 2–10% in 47 (13%) mutations. Mutations were detected in BRAF (42%), NRAS (25%), KIT (4.9%) and PIK3CA (2.7%). The incidence of class-1, class-2 and class-3 mutations were 33% (26% p.V600E and 6.1% p.V600K), 3.1 and 4.9% respectively. With a broader reportable range of NGS, class-1, class-2 and class-3 mutations accounted for 77, 7.4 and 12% of all BRAF mutations. Class-3 mutations, commonly affecting codons 594, 466 and 467, showed a higher incidence of coexisting RAS mutations, consistent with their RAS-dependent signaling. Significant association with old age and primary tumors of head/neck/upper back suggest chronic solar damage as a contributing factor for melanomas harboring BRAF p.V600K or class-3 mutations. Conclusion This study categorizes the range, frequency, coexisting driver mutations and clinical characteristics of the three classes of BRAF mutations in a large cohort of melanomas in a clinical diagnostic setting. Further prospective studies are warranted to elucidate the clinical outcomes and benefits of newly developed targeted therapy in melanoma patients carrying each class of BRAF mutation. Electronic supplementary material The online version of this article (10.1186/s12885-019-5864-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Parvez M Lokhandwala
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.
| | - Li-Hui Tseng
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Erika Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA
| | - Gang Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA
| | - Aparna Pallavajjalla
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.,Departments of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.,Departments of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.
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25
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Abstract
Genetic material derived from tumours is constantly shed into the circulation of cancer patients both in the form of circulating free nucleic acids and within circulating cells or extracellular vesicles. Monitoring cancer-specific genomic alterations, particularly mutant allele frequencies, in circulating nucleic acids allows for a non-invasive liquid biopsy for detecting residual disease and response to therapy. The advent of molecular targeted treatments and immunotherapies with increasing effectiveness requires corresponding effective molecular biology methods for the detection of biomarkers such as circulating nucleic acid to monitor and ultimately personalise therapy. The use of polymerase chain reaction (PCR)-based methods, such as droplet digital PCR, allows for a very sensitive analysis of circulating tumour DNA, but typically only a limited number of gene mutations can be detected in parallel. In contrast, next-generation sequencing allows for parallel analysis of multiple mutations in many genes. The development of targeted next-generation sequencing cancer gene panels optimised for the detection of circulating free DNA now provides both the flexibility of multiple mutation analysis coupled with a sensitivity that approaches or even matches droplet digital PCR. In this review, we discuss the advantages and disadvantages of these current molecular technologies in conjunction with how this field is evolving in the context of melanoma diagnosis, prognosis, and monitoring of response to therapy.
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26
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Variability of Bad Prognosis in Uveal Melanoma. Ophthalmol Retina 2018; 3:186-193. [PMID: 31014770 DOI: 10.1016/j.oret.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 02/03/2023]
Abstract
TOPIC Survival of patients with uveal melanoma classified to have a bad prognosis. CLINICAL RELEVANCE To explore reasons for reported variability in survival of patients with uveal melanoma classified to have a bad prognosis. METHODS We searched PUBMED, MEDLINE, and EMBASE for studies reporting survival data for uveal melanoma undergoing prognostic testing with chromosome 3 status by fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), microsatellite analysis (MSA), multiplex ligation-dependent probe amplification (MLPA), single nucleotide polymorphism (SNP), gene expression profiling (GEP) class, and exon sequencing. Only studies reporting 1-year, 3-year, or 5-year survival were included in the study. RESULTS The initial search resulted in 49 studies. Only 12 studies met inclusion criteria. Three studies reported survival data for FISH, 1 study reported survival data for CGH, 1 study reported survival data for MSA, 3 studies reported survival data for MLPA, 3 studies reported survival data for SNP, 3 studies reported survival data for GEP, and 2 studies reported survival data for a combination of tests. No studies reported survival data for exon sequencing. Six studies reported percent free of metastatic death, 2 studies reported metastasis-free survival (MFS), 2 studies reported overall survival (OS), and 2 studies reported probability of metastasis. Metastasis-free survival (5 years) for monosomy 3 by FISH was 40% to 60%, by MLPA was 30% to 40%, by SNP was 72%, and for GEP class 2 was not reported. Overall survival (5 years) for monosomy 3 and disomy 8 tumors by MLPA and GEP class 2 were not comparable (81% and 55%, respectively). CONCLUSIONS Variability exists in reported survival for uveal melanoma with a bad prognosis. Several factors, including composition of study population (tumor size, exclusion of iris melanoma, duration of median follow-up), method of obtaining tumor sample, type of prognostic test, and use of variable outcome measures, can explain some of the observed differences in survival. Variations in determining the cause of death (metastatic or nonmetastatic) may be the major reason for the observed differences. Standardization of study methods and outcome measures will allow comparison of survival data derived from different prognostic tests.
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27
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Zhu ML, Zhou L, Sadri N. Comparison of targeted next generation sequencing (NGS) versus isolated BRAF V600E analysis in patients with metastatic melanoma. Virchows Arch 2018; 473:371-377. [PMID: 29926184 DOI: 10.1007/s00428-018-2393-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/05/2018] [Accepted: 06/12/2018] [Indexed: 12/22/2022]
Abstract
Molecular testing on advanced metastatic melanoma is critical for guiding targeted therapy. Traditionally, this analysis has relied on isolated BRAF V600E analysis; however, more recently targeted next generation sequencing (NGS) is being utilized. The clinical utility of BRAF V600E allele-specific PCR and targeted NGS were compared for metastatic melanoma samples sent to UHCMC pathology during a two and half year span. In two thirds of cases, negative for BRAF V600E, additional mutations were detected that may stratify patients for potential or approved targeted therapies. Targeted-NGS testing is feasible and cost-affordable and provides additional potentially actionable information for patients with BRAF V600E/K negative metastatic melanoma. Based on this analysis, we have adopted to screen patients with advanced melanoma with allele-specific V600E/K PCR and reflex negative cases for targeted NGS to maximize patient benefit.
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Affiliation(s)
- Meng-Lei Zhu
- Department of Pathology and Laboratory Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, 7100 Euclid Avenue, Cleveland, OH, 44103, USA
| | - Lan Zhou
- Department of Pathology and Laboratory Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, 7100 Euclid Avenue, Cleveland, OH, 44103, USA
| | - Navid Sadri
- Department of Pathology and Laboratory Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Department of Pathology, University Hospitals Cleveland Medical Center, 7100 Euclid Avenue, Cleveland, OH, 44103, USA.
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28
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Williams HL, Walsh K, Diamond A, Oniscu A, Deans ZC. Validation of the Oncomine ™ focus panel for next-generation sequencing of clinical tumour samples. Virchows Arch 2018; 473:489-503. [PMID: 30105577 PMCID: PMC6182325 DOI: 10.1007/s00428-018-2411-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/25/2018] [Accepted: 07/09/2018] [Indexed: 01/01/2023]
Abstract
The clinical utility of next-generation sequencing (NGS) for a diverse range of targets is expanding, increasing the need for multiplexed analysis of both DNA and RNA. However, translation into daily use requires a rigorous and comprehensive validation strategy. The aim of this clinical validation was to assess the performance of the Ion Torrent Personal Genome Machine (IonPGM™) and validate the Oncomine™ Focus DNA and RNA Fusion panels for clinical application in solid tumour testing of formalin-fixed, paraffin-embedded (FFPE) tissue. Using a mixture of routine FFPE and reference material across a variety of tissue and specimen types, we sequenced 86 and 31 samples on the Oncomine™ Focus DNA and RNA Fusion assays, respectively. This validation considered a number of parameters including the clinical robustness of the bioinformatics pipeline for variant detection and interpretation. The Oncomine™ Focus DNA assay had a sample and variant-based sensitivity of 99.1 and 97.1%, respectively, and an assay specificity of 100%. The Oncomine™ Focus Fusion panel had a good sensitivity and specificity based upon the samples assessed, however requires further validation to confirm findings due to limited sample numbers. We observed a good sequencing performance based upon amplicon, gene (hotspot variants within gene) and sample specific analysis with 92% of clinical samples obtaining an average amplicon coverage above 500X. Detection of some indels was challenging for the routine IonReporter™ workflow; however, the addition of NextGENe® software improved indel identification demonstrating the importance of both bench and bioinformatic validation. With an increasing number of clinically actionable targets requiring a variety of methodologies, NGS provides a cost-effective and time-saving methodology to assess multiple targets across different modalities. We suggest the use of multiple analysis software to ensure identification of clinically applicable variants.
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Affiliation(s)
- Hannah L Williams
- UKNEQAS for Molecular Genetics, Royal Infirmary of Edinburgh, Edinburgh, UK.
- NHS Lothian, Department of Molecular Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK.
- University of St Andrews, School of Medicine, North Haugh, St Andrews, Fife, KY16 9TF, UK.
| | - Kathy Walsh
- NHS Lothian, Department of Molecular Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Austin Diamond
- NHS Lothian, Molecular Genetics, Western General Hospital, Edinburgh, UK
| | - Anca Oniscu
- NHS Lothian, Department of Molecular Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Zandra C Deans
- UKNEQAS for Molecular Genetics, Royal Infirmary of Edinburgh, Edinburgh, UK
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29
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Eastley NC, Ottolini B, Neumann R, Luo JL, Hastings RK, Khan I, Moore DA, Esler CP, Shaw JA, Royle NJ, Ashford RU. Circulating tumour-derived DNA in metastatic soft tissue sarcoma. Oncotarget 2018; 9:10549-10560. [PMID: 29535826 PMCID: PMC5828212 DOI: 10.18632/oncotarget.24278] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 01/09/2018] [Indexed: 01/08/2023] Open
Abstract
Following treatment 40% of soft tissue sarcoma (STS) patients suffer disease recurrence. In certain cancers circulating cell free DNA (cfDNA) and circulating tumour-derived DNA (ctDNA) characteristics correlate closely with disease burden, making them exciting potential sources of biomarkers. Despite this, the circulating nucleic acid characteristics of only 2 STS patients have been reported to date. To address this we used an Ion AmpliSeq™ panel custom specifically designed for STS patients to conduct a genetic characterisation of plasma cfDNA, buffy coat (germline) DNA and where available Formalin-Fixed Paraffin-Embedded (FFPE) primary STS tissue DNA in a cohort of 11 metastatic STS patients. We found that total cfDNA levels were significantly elevated in the STS patients analysed, and weakly correlated with disease burden. Using our Ion AmpliSeq™ panel we also successfully detected ctDNA in 4/11 (36%) patients analysed with a wide variety of STS subtypes and disease burdens. This evidence included the presence of cancer associated TP53 / PIK3CA mutations in 2 patients' plasma and matched primary STS tumour tissue, and in the plasma alone for 2 patients. We also identified 2 potential examples of allelic loss of heterozygosity in an additional patient's STS DNA and cfDNA. This is the largest study performed characterising STS patient cfDNA/ctDNA and confirms that the field remains an attractive potential source of novel STS biomarkers. Further work is required to investigate the circulating nucleic acid characteristics of individual STS subtypes, and the potential prognostic or therapeutic roles that cfDNA/ctDNA may hold for patients with these complex tumours.
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Affiliation(s)
- Nicholas C. Eastley
- University Hospitals of Leicester NHS Trust, Trauma and Orthopaedics, Leicester, UK
- University of Leicester Department of Genetics, Leicester, UK
| | - Barbara Ottolini
- University of Leicester Department of Cancer Studies, Leicester, UK
| | - Rita Neumann
- University of Leicester Department of Genetics, Leicester, UK
| | - Jin-Li Luo
- University of Leicester Department of Cancer Studies, Leicester, UK
| | | | - Imran Khan
- University Hospitals of Leicester NHS Trust, Trauma and Orthopaedics, Leicester, UK
| | - David A. Moore
- University of Leicester Department of Cancer Studies, Leicester, UK
| | | | | | - Nicola J. Royle
- University of Leicester Department of Genetics, Leicester, UK
| | - Robert U. Ashford
- University Hospitals of Leicester NHS Trust, Trauma and Orthopaedics, Leicester, UK
- Nottingham University Hospitals NHS Trust, Nottingham, UK
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30
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Somatic mutation analysis in melanoma using targeted next generation sequencing. Exp Mol Pathol 2017; 103:172-177. [PMID: 28822769 DOI: 10.1016/j.yexmp.2017.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 01/22/2023]
Abstract
Advanced stage malignant melanoma often responds poorly to therapy with low survival rates. New therapeutic approaches are based upon a growing understanding of the underlying molecular abnormalities. We demonstrate the feasibility of a next generation sequencing (NGS) assay, which targets hotspots in 50 cancer genes, to assess genotypes that may influence therapeutic selection and response. DNA was extracted from formalin fixed paraffin embedded (FFPE) melanoma specimens to create multiplexed libraries which were sequenced. Of the 121 cases, BRAF mutations were present in 48 cases (40%) and NRAS mutations in 24 cases (20%). We identified other gene variants in 20 BRAF-mutated cases. Additional gene variants were also identified in the 57 BRAF wild-type cases. Four patients harbored different gene mutations at metastatic sites as compared to their primary lesions or metastasis from different sites. Concurrent gene variants may provide additional targets for future therapies and may suggest alternative mechanisms of secondary resistance.
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31
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Álvarez-Rodríguez B, Latorre A, Posch C, Somoza Á. Recent advances in uveal melanoma treatment. Med Res Rev 2017; 37:1350-1372. [PMID: 28759124 DOI: 10.1002/med.21460] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 06/21/2017] [Accepted: 06/23/2017] [Indexed: 12/16/2022]
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Recent advances in the understanding of molecular characteristics helped to determine which tumors are most likely to progress. About 50% of patients carrying genetic alterations such as chromosomal aberrations and mutations are at significant risk for metastatic disease of which the majority will succumb to UM within few months. Currently, there is no effective treatment for metastatic uveal melanoma, and we hope this review will encourage researchers and clinicians to work to find a better standard of care. In this article we provide a comprehensive overview of the molecular framework of UM, highlighting the most common mutations involved in this kind of cancer. It also covers the most recent treatments from basic research to clinical trials, including small molecules, nucleic acids or immunotherapy, among others. It is intended to serve as a key reference for clinicians and researchers working in this field.
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Affiliation(s)
- Beatriz Álvarez-Rodríguez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), CNB-CSIC-IMDEA Nanociencia Associated Unit "Unidad de Nanobiotecnología,", Madrid, Spain
| | - Alfonso Latorre
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), CNB-CSIC-IMDEA Nanociencia Associated Unit "Unidad de Nanobiotecnología,", Madrid, Spain
| | - Christian Posch
- Department of Dermatology and Venerology, Rudolfstiftung Hospital, Vienna, Austria.,School of Medicine, Sigmund Freud University, Vienna, Austria
| | - Álvaro Somoza
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), CNB-CSIC-IMDEA Nanociencia Associated Unit "Unidad de Nanobiotecnología,", Madrid, Spain
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