1
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Taneyama Y, Morimoto A, Ochiai H, Ando K, Kakuda H, Naruke Y, Yokoi S. Trametinib for a child with refractory Rosai-Dorfman-Destombes disease harboring a novel somatic mutation in MAP2K1. Int J Hematol 2024:10.1007/s12185-024-03818-9. [PMID: 39003680 DOI: 10.1007/s12185-024-03818-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
Rosai-Dorfman-Destombes disease (RDD) is a rare histiocytosis characterized by accumulation of S100 + , CD68 + , and CD1a- histiocytes, with emperipolesis. It occurs predominantly in black adolescents and young adults, but rarely in Japanese children. Recently, oncogenic mutations in mitogen-activated protein kinase (MAPK) pathway genes were reported in 30-50% of patients with RDD, and several studies have described treatment of adult patients with MAPK inhibitors. Here, we present the case of a Japanese boy with refractory RDD without signs of cardiofaciocutaneous (CFC) syndrome who harbored MAP2K1 p.Lys59del and responded to trametinib. The patient had lymph node, nasal cavity, kidney, upper respiratory tract, and intracranial involvement. RDD progressed after multi-agent chemotherapy, but responded to trametinib (0.025 mg/kg). Trametinib did not eliminate the mass lesions, but trametinib plus minimal prednisolone (0.1 mg/kg) resulted in a good outcome for more than 15 months, without significant adverse effects. MAP2K1 p.Lys59del has been described as a germline mutation in a patient with CFC syndrome, but not as a somatic mutation in patients with malignancies. Trametinib may be a promising drug for children with RDD that is refractory to multi-agent chemotherapy. Its long-term efficacy and safety alone and in combination with chemotherapy should be investigated.
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Affiliation(s)
- Yuichi Taneyama
- Department of Hematology/Oncology, Chiba Children's Hospital, Chiba, Japan
| | - Akira Morimoto
- Division of Pediatrics, Showa Inan General Hospital, 3232 Akaho , Komagane, Nagano, 399-4117, Japan.
- Department of Pediatrics, Jichi Medical University School of Medicine, Shimotsuke, Japan.
| | - Hidemasa Ochiai
- Department of Hematology/Oncology, Chiba Children's Hospital, Chiba, Japan
| | - Kumiko Ando
- Department of Hematology/Oncology, Chiba Children's Hospital, Chiba, Japan
| | - Harumi Kakuda
- Department of Hematology/Oncology, Chiba Children's Hospital, Chiba, Japan
| | - Yuki Naruke
- Department of Pathology, Chiba Children's Hospital, Chiba, Japan
| | - Sana Yokoi
- Division of Genetic Diagnostics and Cancer Genome Center, Chiba Cancer Center, Chiba, Japan
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2
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Response and Resistance to Trametinib in MAP2K1-Mutant Triple-Negative Melanoma. Int J Mol Sci 2023; 24:ijms24054520. [PMID: 36901951 PMCID: PMC10003177 DOI: 10.3390/ijms24054520] [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: 01/19/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
The development of targeted therapies for non-BRAF p.Val600-mutant melanomas remains a challenge. Triple wildtype (TWT) melanomas that lack mutations in BRAF, NRAS, or NF1 form 10% of human melanomas and are heterogeneous in their genomic drivers. MAP2K1 mutations are enriched in BRAF-mutant melanoma and function as an innate or adaptive resistance mechanism to BRAF inhibition. Here we report the case of a patient with TWT melanoma with a bona fide MAP2K1 mutation without any BRAF mutations. We performed a structural analysis to validate that the MEK inhibitor trametinib could block this mutation. Although the patient initially responded to trametinib, he eventually progressed. The presence of a CDKN2A deletion prompted us to combine a CDK4/6 inhibitor, palbociclib, with trametinib but without clinical benefit. Genomic analysis at progression showed multiple novel copy number alterations. Our case illustrates the challenges of combining MEK1 and CDK4/6 inhibitors in case of resistance to MEK inhibitor monotherapy.
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3
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Qin S, Gao H, Kim W, Zhang H, Gu Y, Kalari KR, Sinnwell JP, Scholz JA, Xie F, Yin P, Yu J, Qin B, Zhuang Y, Wei L, Tan W, Bryce AH, Weinshilboum RM, Wang L. Biomarkers for Predicting Abiraterone Treatment Outcome and Selecting Alternative Therapies in Castration-Resistant Prostate Cancer. Clin Pharmacol Ther 2022; 111:1296-1306. [PMID: 35288936 PMCID: PMC9124371 DOI: 10.1002/cpt.2582] [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: 11/02/2021] [Accepted: 03/10/2022] [Indexed: 11/07/2022]
Abstract
Approximately one‐third of patients with metastatic castration‐resistant prostate cancer (CRPC) exhibited primary abiraterone resistance. To identify alternative treatment for abiraterone nonresponders, we performed drug discovery analyses using the L1000 database using differentially expressed genes identified in tumor biopsies and patient‐derived xenograft (PDX) tumors between abiraterone responders and nonresponders enrolled in PROMOTE trial. This approach identified 3 drugs, including topoisomerase II (TOP2) inhibitor mitoxantrone, CDK4/6 inhibitor palbociclib, and pan‐CDK inhibitor PHA‐793887. These drugs significantly suppressed the growth of abiraterone‐resistant cell lines and PDX models. Moreover, we identified 11 genes targeted by all 3 drugs that were associated with worse outcomes in both the PROMOTE and Stand Up To Cancer cohorts. This 11‐gene panel might also function as biomarkers to select the 3 alternative therapies for this subgroup of patients with CRPC, warranting further clinical investigation.
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Affiliation(s)
- Sisi Qin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Wootae Kim
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Huan Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Yayun Gu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Jason P Sinnwell
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Jodi A Scholz
- Department of Comparative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Fang Xie
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Ping Yin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Bo Qin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Yongxian Zhuang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Lixuan Wei
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Winston Tan
- Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Alan H Bryce
- Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Phoenix, Arizona, USA
| | - Richard M Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
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4
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Remenár É, Dóczi R, Dirner A, Sipos A, Perjési A, Tihanyi D, Vodicska B, Lakatos D, Horváth K, Kajáry K, Schwáb R, Déri J, Lengyel CG, Várkondi E, Vályi-Nagy I, Peták I. Lasting Complete Clinical Response of a Recurring Cutaneous Squamous Cell Carcinoma With MEK Mutation and PIK3CA Amplification Achieved by Dual Trametinib and Metformin Therapy. JCO Precis Oncol 2022; 6:e2100344. [PMID: 35005996 DOI: 10.1200/po.21.00344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Éva Remenár
- Buda Hospitaller Order of St John of God, Budapest, Hungary
| | - Róbert Dóczi
- Oncompass Medicine Hungary Ltd, Budapest, Hungary
| | - Anna Dirner
- Oncompass Medicine Hungary Ltd, Budapest, Hungary
| | - Anna Sipos
- Oncompass Medicine Hungary Ltd, Budapest, Hungary
| | | | - Dóra Tihanyi
- Oncompass Medicine Hungary Ltd, Budapest, Hungary
| | | | - Dóra Lakatos
- Oncompass Medicine Hungary Ltd, Budapest, Hungary
| | | | | | - Richárd Schwáb
- Oncompass Medicine Hungary Ltd, Budapest, Hungary.,MiND Klinika Kft, Budapest, Hungary
| | - Júlia Déri
- Oncompass Medicine Hungary Ltd, Budapest, Hungary
| | | | | | - István Vályi-Nagy
- Centrum Hospital of Southern Pest, National Hematology and Infectology Institute, Budapest, Hungary
| | - István Peták
- Oncompass Medicine Hungary Ltd, Budapest, Hungary.,Department of Pharmacology, Semmelweis University, Budapest, Hungary.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL
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5
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Yamamoto S, Yano S, Kinoshita M, Suzuki S. In Situ Pinpoint Photopolymerization of Phos-Tag Polyacrylamide Gel in Poly(dimethylsiloxane)/Glass Microchip for Specific Entrapment, Derivatization, and Separation of Phosphorylated Compounds. Gels 2021; 7:gels7040268. [PMID: 34940328 PMCID: PMC8701177 DOI: 10.3390/gels7040268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
An improved method for the online preconcentration, derivatization, and separation of phosphorylated compounds was developed based on the affinity of a Phos-tag acrylamide gel formed at the intersection of a polydimethylsiloxane/glass multichannel microfluidic chip toward these compounds. The acrylamide solution comprised Phos-tag acrylamide, acrylamide, and N,N-methylene-bis-acrylamide, while 2,2′-azobis[2-methyl-N-(2-hydroxyethyl)propionamide] was used as a photocatalytic initiator. The Phos-tag acrylamide gel was formed around the channel crossing point via irradiation with a 365 nm LED laser. The phosphorylated peptides were specifically concentrated in the Phos-tag acrylamide gel by applying a voltage across the gel plug. After entrapment of the phosphorylated compounds in the Phos-tag acrylamide gel, 5-(4,6-dichlorotriazinyl)aminofluorescein (DTAF) was introduced to the gel for online derivatization of the concentrated phosphorylated compounds. The online derivatized DTAF-labeled phosphorylated compounds were eluted by delivering a complex of phosphate ions and ethylenediamine tetraacetic acid as the separation buffer. This method enabled sensitive analysis of the phosphorylated peptides.
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Affiliation(s)
- Sachio Yamamoto
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashiosaka 577-8502, Osaka, Japan; (S.Y.); (M.K.); (S.S.)
- Correspondence:
| | - Shoko Yano
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashiosaka 577-8502, Osaka, Japan; (S.Y.); (M.K.); (S.S.)
| | - Mitsuhiro Kinoshita
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashiosaka 577-8502, Osaka, Japan; (S.Y.); (M.K.); (S.S.)
| | - Shigeo Suzuki
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashiosaka 577-8502, Osaka, Japan; (S.Y.); (M.K.); (S.S.)
- Antiaging Center, Kindai University, 3-4-1 Kowakae, Higashiosaka 577-8502, Osaka, Japan
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6
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Tanaka N, Lin JJ, Li C, Ryan MB, Zhang J, Kiedrowski LA, Michel AG, Syed MU, Fella KA, Sakhi M, Baiev I, Juric D, Gainor JF, Klempner SJ, Lennerz JK, Siravegna G, Bar-Peled L, Hata AN, Heist RS, Corcoran RB. Clinical Acquired Resistance to KRAS G12C Inhibition through a Novel KRAS Switch-II Pocket Mutation and Polyclonal Alterations Converging on RAS-MAPK Reactivation. Cancer Discov 2021; 11:1913-1922. [PMID: 33824136 DOI: 10.1158/2159-8290.cd-21-0365] [Citation(s) in RCA: 234] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023]
Abstract
Mutant-selective KRASG12C inhibitors, such as MRTX849 (adagrasib) and AMG 510 (sotorasib), have demonstrated efficacy in KRAS G12C-mutant cancers, including non-small cell lung cancer (NSCLC). However, mechanisms underlying clinical acquired resistance to KRASG12C inhibitors remain undetermined. To begin to define the mechanistic spectrum of acquired resistance, we describe a patient with KRAS G12C NSCLC who developed polyclonal acquired resistance to MRTX849 with the emergence of 10 heterogeneous resistance alterations in serial cell-free DNA spanning four genes (KRAS, NRAS, BRAF, MAP2K1), all of which converge to reactivate RAS-MAPK signaling. Notably, a novel KRAS Y96D mutation affecting the switch-II pocket, to which MRTX849 and other inactive-state inhibitors bind, was identified that interferes with key protein-drug interactions and confers resistance to these inhibitors in engineered and patient-derived KRAS G12C cancer models. Interestingly, a novel, functionally distinct tricomplex KRASG12C active-state inhibitor RM-018 retained the ability to bind and inhibit KRASG12C/Y96D and could overcome resistance. SIGNIFICANCE: In one of the first reports of clinical acquired resistance to KRASG12C inhibitors, our data suggest polyclonal RAS-MAPK reactivation as a central resistance mechanism. We also identify a novel KRAS switch-II pocket mutation that impairs binding and drives resistance to inactive-state inhibitors but is surmountable by a functionally distinct KRASG12C inhibitor.See related commentary by Pinnelli and Trusolino, p. 1874.This article is highlighted in the In This Issue feature, p. 1861.
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Affiliation(s)
- Noritaka Tanaka
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Chendi Li
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Meagan B Ryan
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Junbing Zhang
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Alexa G Michel
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Mohammed U Syed
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Katerina A Fella
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Mustafa Sakhi
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Islam Baiev
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Samuel J Klempner
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Giulia Siravegna
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Liron Bar-Peled
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts.
| | - Rebecca S Heist
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts.
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts.
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7
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Ji J, Kaneva K, Hiemenz MC, Dhall G, Davidson TB, Erdreich-Epstein A, Hawes D, Hurth K, Margol AS, Mathew AJ, Robison NJ, Schmidt RJ, Tran HN, Judkins AR, Cotter JA, Biegel JA. Clinical utility of comprehensive genomic profiling in central nervous system tumors of children and young adults. Neurooncol Adv 2021; 3:vdab037. [PMID: 33948563 PMCID: PMC8080244 DOI: 10.1093/noajnl/vdab037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Recent large-scale genomic studies have revealed a spectrum of genetic variants associated with specific subtypes of central nervous system (CNS) tumors. The aim of this study was to determine the clinical utility of comprehensive genomic profiling of pediatric, adolescent and young adult (AYA) CNS tumors in a prospective setting, including detection of DNA sequence variants, gene fusions, copy number alterations (CNAs), and loss of heterozygosity. Methods OncoKids, a comprehensive DNA- and RNA-based next-generation sequencing (NGS) panel, in conjunction with chromosomal microarray analysis (CMA) was employed to detect diagnostic, prognostic, and therapeutic markers. NGS was performed on 222 specimens from 212 patients. Clinical CMA data were analyzed in parallel for 66% (146/222) of cases. Results NGS demonstrated clinically significant alterations in 66% (147/222) of cases. Diagnostic markers were identified in 62% (138/222) of cases. Prognostic information and targetable genomic alterations were identified in 22% (49/222) and 18% (41/222) of cases, respectively. Diagnostic or prognostic CNAs were revealed by CMA in 69% (101/146) of cases. Importantly, clinically significant CNAs were detected in 57% (34/60) of cases with noncontributory NGS results. Germline cancer predisposition testing was indicated for 27% (57/212) of patients. Follow-up germline testing was performed for 20 patients which confirmed a germline pathogenic/likely pathogenic variant in 9 cases: TP53 (2), NF1 (2), SMARCB1 (1), NF2 (1), MSH6 (1), PMS2 (1), and a patient with 47,XXY Klinefelter syndrome. Conclusions Our results demonstrate the significant clinical utility of integrating genomic profiling into routine clinical testing for pediatric and AYA patients with CNS tumors.
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Affiliation(s)
- Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Kristiyana Kaneva
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Matthew C Hiemenz
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Girish Dhall
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Division of Pediatric Hematology-Oncology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tom Belle Davidson
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Anat Erdreich-Epstein
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA.,Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Debra Hawes
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Kyle Hurth
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Ashley S Margol
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Anna J Mathew
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Nathan J Robison
- Division of Hematology-Oncology, Cancer and Blood Disease Institute and Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Hung N Tran
- Kaiser Permanente Los Angeles Medical Center, Los Angeles, California, USA
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Jennifer A Cotter
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine of University of Southern California, Los Angeles, California, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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8
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Kinoshita E, Kinoshita-Kikuta E, Koike T. Determining Protein Phosphorylation Status Using Antibody Arrays and Phos-Tag Biotin. Methods Mol Biol 2020; 2237:217-224. [PMID: 33237421 DOI: 10.1007/978-1-0716-1064-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
We describe here a standard protocol for determining the phosphorylation status of protein multiplexes using antibody arrays and a biotinylated Phos-tag with a dodeca(ethylene glycol) spacer (Phos-tag Biotin). The procedure is based on an antibody microarray technique used in conjunction with an enhanced chemiluminescence system, and it permits the simultaneous and highly sensitive detection of multiple phosphoproteins in a cell lysate. By using this procedure, we have demonstrated the quantitative detection of the entire phosphorylation status of a target protein involved in intracellular signaling.
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Affiliation(s)
- Eiji Kinoshita
- Department of Functional Molecular Science, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
| | - Emiko Kinoshita-Kikuta
- Department of Functional Molecular Science, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tohru Koike
- Department of Functional Molecular Science, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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9
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Louveau B, Jouenne F, Têtu P, Sadoux A, Gruber A, Lopes E, Delyon J, Serror K, Marco O, Da Meda L, Ndiaye A, Lermine A, Dumaz N, Battistella M, Baroudjian B, Lebbe C, Mourah S. A Melanoma-Tailored Next-Generation Sequencing Panel Coupled with a Comprehensive Analysis to Improve Routine Melanoma Genotyping. Target Oncol 2020; 15:759-771. [PMID: 33151472 DOI: 10.1007/s11523-020-00764-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Tumor molecular deciphering is crucial in clinical management. Pan-cancer next-generation sequencing panels have moved towards exhaustive molecular characterization. However, because of treatment resistance and the growing emergence of pharmacological targets, tumor-specific customized panels are needed to guide therapeutic strategies. OBJECTIVE The objective of this study was to present such a customized next-generation sequencing panel in melanoma. METHODS Melanoma patients with somatic molecular profiling performed as part of routine care were included. High-throughput sequencing was performed with a melanoma tailored next-generation sequencing panel of 64 genes involved in molecular classification, prognosis, theranostic, and therapeutic resistance. Single nucleotide variants and copy number variations were screened, and a comprehensive molecular analysis identified clinically relevant alterations. RESULTS Four hundred and twenty-one melanoma cases were analyzed (before any treatment initiation for 94.8% of patients). After bioinformatic prioritization, we uncovered 561 single nucleotide variants, 164 copy number variations, and four splice-site mutations. At least one alteration was detected in 368 (87.4%) lesions, with BRAF, NRAS, CDKN2A, CCND1, and MET as the most frequently altered genes. Among patients with BRAFV600 mutated melanoma, 44.5% (77 of 173) harbored at least one concurrent alteration driving potential resistance to mitogen-activated protein kinase inhibitors. In patients with RAS hotspot mutated lesions and in patients with neither BRAFV600 nor RAS hotspot mutations, alterations constituting potential pharmacological targets were found in 56.9% (66 of 116) and 47.7% (63 of 132) of cases, respectively. CONCLUSIONS Our tailored next-generation sequencing assay coupled with a comprehensive analysis may improve therapeutic management in a significant number of patients with melanoma. Updating such a panel and implementing multi-omic approaches will further enhance patients' clinical management.
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Affiliation(s)
- Baptiste Louveau
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France.,Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France
| | - Fanélie Jouenne
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France.,Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France
| | - Pauline Têtu
- Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Aurélie Sadoux
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France
| | - Aurélia Gruber
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France
| | - Eddie Lopes
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France
| | - Julie Delyon
- Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.,Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Kevin Serror
- Department of Plastic, Reconstructive and Esthetic Surgery, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Oren Marco
- Department of Plastic, Reconstructive and Esthetic Surgery, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laetitia Da Meda
- Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Aminata Ndiaye
- MOABI-APHP Bioinformatics Platform-WIND-DSI, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alban Lermine
- MOABI-APHP Bioinformatics Platform-WIND-DSI, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nicolas Dumaz
- INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France
| | - Maxime Battistella
- Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.,Department of Pathology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Barouyr Baroudjian
- Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Céleste Lebbe
- Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.,Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Samia Mourah
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France. .,Université de Paris, Paris, France. .,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.
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