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Mirek J, Bal W, Olbryt M. Melanoma genomics - will we go beyond BRAF in clinics? J Cancer Res Clin Oncol 2024; 150:433. [PMID: 39340537 PMCID: PMC11438618 DOI: 10.1007/s00432-024-05957-2] [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: 07/26/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024]
Abstract
In the era of next-generation sequencing, the genetic background of cancer, including melanoma, appears to be thoroughly established. However, evaluating the oncogene BRAF mutation in codon V600 is still the only companion diagnostic genomic test commonly implemented in clinics for molecularly targeted treatment of advanced melanoma. Are we wasting the collected genomic data? Will we implement our current genomic knowledge of melanoma in clinics soon? This question is rather urgent because new therapeutic targets and biomarkers are needed to implement more personalized, patient-tailored therapy in clinics. Here, we provide an update on the molecular background of melanoma, including a description of four already established molecular subtypes: BRAF+, NRAS+, NF1+, and triple WT, as well as relatively new NGS-derived melanoma genes such as PREX2, ERBB4, PPP6C, FBXW7, PIK3CA, and IDH1. We also present a comparison of genomic profiles obtained in recent years with a focus on the most common melanoma genes. Finally, we propose our melanoma gene panel consisting of 22 genes that, in our opinion, are "must-have" genes in both melanoma-specific genomic tests and pan-cancer tests established to improve the treatment of melanoma further.
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Affiliation(s)
- Justyna Mirek
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, Gliwice, 44-101, Poland
| | - Wiesław Bal
- Chemotherapy Day Unit, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, Gliwice, 44-101, Poland
| | - Magdalena Olbryt
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, Gliwice, 44-101, Poland.
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2
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Steiner S, Pliego-Mendieta A, Haberecker M, Hussung S, Kollár A, Fritsch R, Arnold F, Lenggenhager D, Planas-Paz L, Pauli C. Ex vivo modeling of acquired drug resistance in BRAF - mutated pancreatic cancer organoids uncovers individual therapeutic vulnerabilities. Cancer Lett 2024; 584:216650. [PMID: 38246222 DOI: 10.1016/j.canlet.2024.216650] [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: 07/24/2023] [Revised: 12/21/2023] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis due to late detection and limited treatment options. Some PDAC patients harbor alterations that qualify for targeted treatment strategies but develop acquired resistance, leading to treatment failure. We here report the ex vivo modeling of acquired drug resistance by creating a PDAC patient-derived tumor organoid (PDTO) model harboring a rare BRAF R506_K507ins VLR mutation resulting in a resistance to trametinib, a MEK inhibitor. Genomic and transcriptomic analyses revealed upregulated WNT signaling in resistant PDTO clones compared to treatment-naïve parental control cells. By combining genomic and transcriptomic analysis with a functional drug testing approach, we uncovered a de novo upregulation and circumventive reliance on WNT signaling in resistant PDTO clones. Ex vivo models such as PDTOs represent valuable tools for resistance modelling and offer the discovery of novel therapeutic approaches for patients in need where clinical diagnostic tools are currently at the limit.
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Affiliation(s)
- Sabrina Steiner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - Alicia Pliego-Mendieta
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - Martina Haberecker
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - Saskia Hussung
- Department of Hematology and Oncology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Anna Kollár
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - Ralph Fritsch
- Department of Hematology and Oncology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Fabian Arnold
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - Daniela Lenggenhager
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - Lara Planas-Paz
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091, Zurich, Switzerland; Medical Faculty, University of Zurich, Pestalozzistrasse 3, 8032, Zurich, Switzerland.
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3
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Millán-Esteban D, Peña-Chilet M, García-Casado Z, Manrique-Silva E, Requena C, Bañuls J, López-Guerrero JA, Rodríguez-Hernández A, Traves V, Dopazo J, Virós A, Kumar R, Nagore E. Mutational Characterization of Cutaneous Melanoma Supports Divergent Pathways Model for Melanoma Development. Cancers (Basel) 2021; 13:5219. [PMID: 34680367 PMCID: PMC8533762 DOI: 10.3390/cancers13205219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
According to the divergent pathway model, cutaneous melanoma comprises a nevogenic group with a propensity to melanocyte proliferation and another one associated with cumulative solar damage (CSD). While characterized clinically and epidemiologically, the differences in the molecular profiles between the groups have remained primarily uninvestigated. This study has used a custom gene panel and bioinformatics tools to investigate the potential molecular differences in a thoroughly characterized cohort of 119 melanoma patients belonging to nevogenic and CSD groups. We found that the nevogenic melanomas had a restricted set of mutations, with the prominently mutated gene being BRAF. The CSD melanomas, in contrast, showed mutations in a diverse group of genes that included NF1, ROS1, GNA11, and RAC1. We thus provide evidence that nevogenic and CSD melanomas constitute different biological entities and highlight the need to explore new targeted therapies.
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Affiliation(s)
- David Millán-Esteban
- School of Medicine, Universidad Católica de València San Vicente Mártir, 46001 Valencia, Spain;
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (Z.G.-C.); (J.A.L.-G.)
| | - María Peña-Chilet
- Clinical Bioinformatics Area, Fundación Progreso y Salud, Hospital Virgen del Rocío, 41013 Sevilla, Spain; (M.P.-C.); (J.D.)
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, 41013 Sevilla, Spain;
| | - Zaida García-Casado
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (Z.G.-C.); (J.A.L.-G.)
| | - Esperanza Manrique-Silva
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (E.M.-S.); (A.R.-H.)
| | - Celia Requena
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, 41013 Sevilla, Spain;
| | - José Bañuls
- Department of Dermatology, El Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Hospital General Universitario de Alicante, 03010 Alicante, Spain;
| | - Jose Antonio López-Guerrero
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (Z.G.-C.); (J.A.L.-G.)
| | - Aranzazu Rodríguez-Hernández
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (E.M.-S.); (A.R.-H.)
| | - Víctor Traves
- Department of Pathological Anatomy, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain;
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud, Hospital Virgen del Rocío, 41013 Sevilla, Spain; (M.P.-C.); (J.D.)
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Sevilla, Spain
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocío, 41013 Sevilla, Spain;
- Fundación Progreso y Salud-ELIXIR-es, Hospital Virgen del Rocío, 41013 Sevilla, Spain
| | - Amaya Virós
- Skin Cancer and Aging Lab, Cancer Research UK Manchester Institute, University of Manchester, Manchester SK10 4TG, UK;
| | - Rajiv Kumar
- Division of Functional Genome Analysis, Deutsches Krebsforschüngzentrum, 69120 Heidelberg, Germany;
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska, 142 20 Prague, Czech Republic
- Institute of Medical Biometry and Informatics, University of Heidelberg, 69117 Heidelberg, Germany
| | - Eduardo Nagore
- School of Medicine, Universidad Católica de València San Vicente Mártir, 46001 Valencia, Spain;
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain; (E.M.-S.); (A.R.-H.)
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4
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NGS Analysis of Liquid Biopsy (LB) and Formalin-Fixed Paraffin-Embedded (FFPE) Melanoma Samples Using Oncomine™ Pan-Cancer Cell-Free Assay. Genes (Basel) 2021; 12:genes12071080. [PMID: 34356096 PMCID: PMC8303399 DOI: 10.3390/genes12071080] [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: 05/31/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) in liquid biopsies may contribute to the diagnosis, monitoring, and personalized therapy of cancer through the real-time detection of a tumor’s genetic profile. There are a few NGS platforms offering high-sensitivity sequencing of cell-free DNA (cfDNA) samples. The aim of this study was to evaluate the Ion AmpliSeq HD Technology for targeted sequencing of tumor and liquid biopsy samples from patients with fourth-stage melanoma. Sequencing of 30 samples (FFPE tumor and liquid biopsy) derived from 14 patients using the Oncomine™ Pan-Cancer Cell-Free Assay was performed. The analysis revealed high concordance between the qPCR and NGS results of the BRAF mutation in FFPE samples (91%), as well as between the FFPE and liquid biopsy samples (91%). The plasma-tumor concordance of the non-BRAF mutations was 28%. A total of 17 pathogenic variants in 14 genes (from 52-gene panel), including TP53, CTNNB1, CCND1, MET, MAP2K1, and GNAS, were identified, with the CTNNB1S45F variant being the most frequent. A positive correlation between the LDH level and cfDNA concentration as well as negative correlation between the LDH level and time to progression was confirmed in a 22-patient cohort. The analysis showed both the potential and limitations of liquid biopsy genetic profiling using HD technology and the Ion Torrent platform.
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5
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Dessources K, Da Cruz Paula A, Pareja F, Stylianou A, Cybulska P, Farmanbar A, Chandarlapaty S, Abu-Rustum NR, Reis-Filho JS, Weigelt B, Mueller JJ. Acquisition of APOBEC Mutagenesis and Microsatellite Instability Signatures in the Development of Brain Metastases in Low-Grade, Early-Stage Endometrioid Endometrial Carcinoma. JCO Precis Oncol 2020; 4:PO.20.00044. [PMID: 33163849 PMCID: PMC7608574 DOI: 10.1200/po.20.00044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anthe Stylianou
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paulina Cybulska
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amir Farmanbar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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6
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Vanni I, Tanda ET, Dalmasso B, Pastorino L, Andreotti V, Bruno W, Boutros A, Spagnolo F, Ghiorzo P. Non-BRAF Mutant Melanoma: Molecular Features and Therapeutical Implications. Front Mol Biosci 2020; 7:172. [PMID: 32850962 PMCID: PMC7396525 DOI: 10.3389/fmolb.2020.00172] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
Melanoma is one of the most aggressive tumors of the skin, and its incidence is growing worldwide. Historically considered a drug resistant disease, since 2011 the therapeutic landscape of melanoma has radically changed. Indeed, the improved knowledge of the immune system and its interactions with the tumor, and the ever more thorough molecular characterization of the disease, has allowed the development of immunotherapy on the one hand, and molecular target therapies on the other. The increased availability of more performing technologies like Next-Generation Sequencing (NGS), and the availability of increasingly large genetic panels, allows the identification of several potential therapeutic targets. In light of this, numerous clinical and preclinical trials are ongoing, to identify new molecular targets. Here, we review the landscape of mutated non-BRAF skin melanoma, in light of recent data deriving from Whole-Exome Sequencing (WES) or Whole-Genome Sequencing (WGS) studies on melanoma cohorts for which information on the mutation rate of each gene was available, for a total of 10 NGS studies and 992 samples, focusing on available, or in experimentation, targeted therapies beyond those targeting mutated BRAF. Namely, we describe 33 established and candidate driver genes altered with frequency greater than 1.5%, and the current status of targeted therapy for each gene. Only 1.1% of the samples showed no coding mutations, whereas 30% showed at least one mutation in the RAS genes (mostly NRAS) and 70% showed mutations outside of the RAS genes, suggesting potential new roads for targeted therapy. Ongoing clinical trials are available for 33.3% of the most frequently altered genes.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | | | - Bruna Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
| | - Andrea Boutros
- Medical Oncology, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genova, Italy
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7
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Tétu P, Delyon J, André J, Reger de Moura C, Sabbah M, Ghanem GE, Battistella M, Mourah S, Lebbé C, Dumaz N. FGF2 Induces Resistance to Nilotinib through MAPK Pathway Activation in KIT Mutated Melanoma. Cancers (Basel) 2020; 12:cancers12051062. [PMID: 32344828 PMCID: PMC7281633 DOI: 10.3390/cancers12051062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022] Open
Abstract
KIT is a bona fide oncogene in a subset of melanoma and, ex vivo, KIT inhibitors are very efficient at killing KIT-mutant melanoma cell lines. However, KIT-mutant melanoma tumors tend to show a de novo resistance in most cases and a limited duration of response when response is achieved. We performed pharmacodynamic studies on patients with KIT-mutated melanoma treated with nilotinib, which suggested that the FGF2 axis may be a mechanism of resistance in this subset of melanoma. Using several melanoma cell lines, which are dependent on oncogenic KIT, we showed that although KIT inhibition markedly decreased cell viability in melanoma cell lines with distinct KIT mutations, this effect was lessened in the presence of FGF2 due to inhibition of BIM expression by MAPK pathway activation. Addition of a MEK inhibitor reversed the FGF2-driven resistance for all KIT mutants. We confirmed the expression of FGF2 and activation of MEK-ERK in melanoma patients using in situ data from a clinical trial. Therefore, the combined inhibition of KIT with FGFR or MEK may be a next-step effective clinical strategy in KIT-mutant melanoma.
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Affiliation(s)
- Pauline Tétu
- INSERM, U976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), F-75010 Paris, France
- Département de Dermatologie, Hôpital Saint Louis, AP-HP, F-75010 Paris, France
| | - Julie Delyon
- INSERM, U976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), F-75010 Paris, France
- Département de Dermatologie, Hôpital Saint Louis, AP-HP, F-75010 Paris, France
| | - Jocelyne André
- INSERM, U976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), F-75010 Paris, France
- Institut de Recherche Saint Louis (IRSL), Université de Paris, F-75010 Paris, France
| | - Coralie Reger de Moura
- INSERM, U976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), F-75010 Paris, France
- Institut de Recherche Saint Louis (IRSL), Université de Paris, F-75010 Paris, France
- Département de Pharmacogénomique, Hôpital Saint Louis, AP-HP, F-75010 Paris, France
| | - Malak Sabbah
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles, Rue Héger-Bordet 1, 1000 Brussels, Belgium
| | - Ghanem E Ghanem
- Laboratory of Oncology and Experimental Surgery, Institut Jules Bordet, Université Libre de Bruxelles, Rue Héger-Bordet 1, 1000 Brussels, Belgium
| | - Maxime Battistella
- INSERM, U976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), F-75010 Paris, France
- Institut de Recherche Saint Louis (IRSL), Université de Paris, F-75010 Paris, France
- Département de Pathologie, Hôpital Saint Louis, AP-HP, F-75010 Paris, France
| | - Samia Mourah
- INSERM, U976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), F-75010 Paris, France
- Institut de Recherche Saint Louis (IRSL), Université de Paris, F-75010 Paris, France
- Département de Pharmacogénomique, Hôpital Saint Louis, AP-HP, F-75010 Paris, France
| | - Céleste Lebbé
- INSERM, U976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), F-75010 Paris, France
- Département de Dermatologie, Hôpital Saint Louis, AP-HP, F-75010 Paris, France
- Institut de Recherche Saint Louis (IRSL), Université de Paris, F-75010 Paris, France
| | - Nicolas Dumaz
- INSERM, U976, Team 1, Human Immunology Pathophysiology & Immunotherapy (HIPI), F-75010 Paris, France
- Institut de Recherche Saint Louis (IRSL), Université de Paris, F-75010 Paris, France
- Correspondence: ; Tel.: +33-01-53-72-20-85
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8
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Hamid AB, Petreaca RC. Secondary Resistant Mutations to Small Molecule Inhibitors in Cancer Cells. Cancers (Basel) 2020; 12:cancers12040927. [PMID: 32283832 PMCID: PMC7226513 DOI: 10.3390/cancers12040927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Secondary resistant mutations in cancer cells arise in response to certain small molecule inhibitors. These mutations inevitably cause recurrence and often progression to a more aggressive form. Resistant mutations may manifest in various forms. For example, some mutations decrease or abrogate the affinity of the drug for the protein. Others restore the function of the enzyme even in the presence of the inhibitor. In some cases, resistance is acquired through activation of a parallel pathway which bypasses the function of the drug targeted pathway. The Catalogue of Somatic Mutations in Cancer (COSMIC) produced a compendium of resistant mutations to small molecule inhibitors reported in the literature. Here, we build on these data and provide a comprehensive review of resistant mutations in cancers. We also discuss mechanistic parallels of resistance.
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Sanna A, Harbst K, Johansson I, Christensen G, Lauss M, Mitra S, Rosengren F, Häkkinen J, Vallon-Christersson J, Olsson H, Ingvar Å, Isaksson K, Ingvar C, Nielsen K, Jönsson G. Tumor genetic heterogeneity analysis of chronic sun-damaged melanoma. Pigment Cell Melanoma Res 2019; 33:480-489. [PMID: 31811783 PMCID: PMC7217060 DOI: 10.1111/pcmr.12851] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/21/2019] [Accepted: 11/29/2019] [Indexed: 12/12/2022]
Abstract
Chronic sun‐damaged (CSD) melanoma represents 10%–20% of cutaneous melanomas and is characterized by infrequent BRAF V600E mutations and high mutational load. However, the order of genetic events or the extent of intra‐tumor heterogeneity (ITH) in CSDhigh melanoma is still unknown. Ultra‐deep targeted sequencing of 40 cancer‐associated genes was performed in 72 in situ or invasive CMM, including 23 CSDhigh cases. In addition, we performed whole exome and RNA sequencing on multiple regions of primary tumor and multiple in‐transit metastases from one CSDhigh melanoma patient. We found no significant difference in mutation frequency in melanoma‐related genes or in mutational load between in situ and invasive CSDhigh lesions, while this difference was observed in CSDlow lesions. In addition, increased frequency of BRAF V600K, NF1, and TP53 mutations (p < .01, Fisher's exact test) was found in CSDhigh melanomas. Sequencing of multiple specimens from one CSDhigh patient revealed strikingly limited ITH with >95% shared mutations. Our results provide evidence that CSDhigh and CSDlow melanomas are distinct molecular entities that progress via different genetic routes.
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Affiliation(s)
- Adriana Sanna
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Katja Harbst
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Iva Johansson
- Department of Clinical Pathology, Skåne University Hospital, Lund, Sweden
| | - Gustav Christensen
- Department of Dermatology, Skåne University Hospital, Lund, Sweden.,Department of Clinical Sciences Lund, Division of Dermatology and Venereology, Lund University, Lund, Sweden
| | - Martin Lauss
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Shamik Mitra
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Frida Rosengren
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Jari Häkkinen
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Johan Vallon-Christersson
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Håkan Olsson
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Åsa Ingvar
- Department of Dermatology, Skåne University Hospital, Lund, Sweden.,Department of Clinical Sciences Lund, Division of Dermatology and Venereology, Lund University, Lund, Sweden
| | - Karolin Isaksson
- Department of Clinical Sciences Lund, Division of Surgery, Skåne University Hospital, Lund University, Lund, Sweden
| | - Christian Ingvar
- Department of Clinical Sciences Lund, Division of Surgery, Skåne University Hospital, Lund University, Lund, Sweden
| | - Kari Nielsen
- Department of Dermatology, Skåne University Hospital, Lund, Sweden.,Department of Clinical Sciences Lund, Division of Dermatology and Venereology, Lund University, Lund, Sweden.,Department of Dermatology, Nordvästra Skåne Teaching Hospital, Lund, Sweden
| | - Göran Jönsson
- Department of Clinical Sciences Lund, Division of Oncology and Pathology, Lund University, Lund, Sweden
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10
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Blanc E, Holtgrewe M, Dhamodaran A, Messerschmidt C, Willimsky G, Blankenstein T, Beule D. Identification and ranking of recurrent neo-epitopes in cancer. BMC Med Genomics 2019; 12:171. [PMID: 31775766 PMCID: PMC6882202 DOI: 10.1186/s12920-019-0611-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/25/2019] [Indexed: 12/25/2022] Open
Abstract
Background Immune escape is one of the hallmarks of cancer and several new treatment approaches attempt to modulate and restore the immune system’s capability to target cancer cells. At the heart of the immune recognition process lies antigen presentation from somatic mutations. These neo-epitopes are emerging as attractive targets for cancer immunotherapy and new strategies for rapid identification of relevant candidates have become a priority. Methods We carefully screen TCGA data sets for recurrent somatic amino acid exchanges and apply MHC class I binding predictions. Results We propose a method for in silico selection and prioritization of candidates which have a high potential for neo-antigen generation and are likely to appear in multiple patients. While the percentage of patients carrying a specific neo-epitope and HLA-type combination is relatively small, the sheer number of new patients leads to surprisingly high reoccurence numbers. We identify 769 epitopes which are expected to occur in 77629 patients per year. Conclusion While our candidate list will definitely contain false positives, the results provide an objective order for wet-lab testing of reusable neo-epitopes. Thus recurrent neo-epitopes may be suitable to supplement existing personalized T cell treatment approaches with precision treatment options.
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Affiliation(s)
- Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Arunraj Dhamodaran
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany
| | - Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Gerald Willimsky
- Institute of Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lindenberger Weg 80, Berlin, 13125, Germany.,Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Thomas Blankenstein
- Institute of Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lindenberger Weg 80, Berlin, 13125, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany.,Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany. .,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany.
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