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Tanaka R, Mrachek K, Arocho-Quinones E, Carlberg VM, Smith C, Kurzrock R, Deshmukh T. Dabrafenib for Pilocytic Astrocytoma With BRAF V599ins. JCO Precis Oncol 2024; 8:e2400055. [PMID: 38781546 DOI: 10.1200/po.24.00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/09/2024] [Indexed: 05/25/2024] Open
Abstract
This report highlights the first pediatric case of pilocytic astrocytoma with BRAF V599ins mutation, successfully treated with dabrafenib.
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Affiliation(s)
- Ryuma Tanaka
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Kelly Mrachek
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI
| | | | | | - Candice Smith
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Razelle Kurzrock
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
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2
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Varachev V, Shekhtman A, Guskov D, Rogozhin D, Zasedatelev A, Nasedkina T. Diagnostics of IDH1/2 Mutations in Intracranial Chondroid Tumors: Comparison of Molecular Genetic Methods and Immunohistochemistry. Diagnostics (Basel) 2024; 14:200. [PMID: 38248076 PMCID: PMC10814347 DOI: 10.3390/diagnostics14020200] [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: 11/20/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/23/2024] Open
Abstract
Intracranial chondroid tumors are a heterogeneous group of neoplasms characterized by the presence of a cartilage matrix. These tumors exhibit overlapping clinical and histological features. Mutations in IDH1/2 genes serve as important diagnostic markers of tumor type, particularly chondrosarcoma. To improve the accuracy of IDH1/2 diagnostics, we compared three methods: biochip assay, real-time PCR with DNA melting analysis using TaqMan probes and sequencing (qPCR-DMA-Sanger), and immunohistochemistry (IHC). Tumor samples from 96 patients were investigated. The IDH1 mutations were detected in 34/64 (53%) chondrosarcomas; IHC detected 27/56 (48.2%) mutations, the qPCR-DMA-Sanger method 27/59 (46%) mutations, and the biochip assay revealed 29/60 (48.3%) mutations. The detection of IDH1 mutations in chordoma (2/15) and osteosarcoma (2/7) suggested the need for a revised diagnosis. In benign tumors, IDH1 mutations were present in chondroma (4/6), but absent in chondromyxoid fibroma (0/4). The most frequent IDH1 mutations were R132C (60%), R132L, and R132G (13.5% each), R132H (8%), and R132S (5%). The concordance between the biochip assay and IHC was 90%, between IHC and PCR-DMA-Sanger 83%, and between biochip assay and qPCR-DMA-Sanger was 98%, respectively. No IDH2 mutations were found. The use of independent diagnostic methods may improve the detection of IDH-mutant specimens in chondroid tumors.
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Affiliation(s)
- Vyacheslav Varachev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (V.V.); (D.G.); (A.Z.)
| | - Anastasia Shekhtman
- N.N. Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, 125047 Moscow, Russia;
- Russian Children’s Clinical Hospital, N.I. Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, 119571 Moscow, Russia;
| | - Dmitrii Guskov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (V.V.); (D.G.); (A.Z.)
| | - Dmitrii Rogozhin
- Russian Children’s Clinical Hospital, N.I. Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, 119571 Moscow, Russia;
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115522 Moscow, Russia
| | - Alexander Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (V.V.); (D.G.); (A.Z.)
| | - Tatiana Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (V.V.); (D.G.); (A.Z.)
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3
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Ryabaya OO, Abramov IS, Khochenkov DA, Akasov R, Sholina NV, Prokofieva AA. Rapamycin synergizes the cytotoxic effects of MEK inhibitor binimetinib and overcomes acquired resistance to therapy in melanoma cell lines in vitro. Invest New Drugs 2021; 39:987-1000. [PMID: 33683500 DOI: 10.1007/s10637-021-01089-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/15/2021] [Indexed: 12/14/2022]
Abstract
Objective The problem of drug resistance to BRAF-targeted therapy often occurs in melanoma treatment. Activation of PI3K/AKT/mTOR signaling pathway is one of the mechanisms of acquired resistance and a potential target for treatment. In the current research, we investigated that dual inhibition of mTOR and MEK synergistically reduced the viability of melanoma cells in vitro. Methods A combination of rapamycin (a macrolide immunosuppressant, mTOR inhibitor) and binimetinib (an anti-cancer small molecule, selective inhibitor of MEK) was studied using a panel of melanoma cell lines, including patient-derived cells. Results It was found, that combinatorial therapy of rapamycin (250 nM) and binimetinib (2 μM) resulted in 25% of cell viability compared to either rapamycin (85%) or binimetinib alone (50%) for A375 and vemurafenib-resistant Mel IL/R cells. The suppressed activation of mTOR and MEK by combined rapamycin and binimetinib treatment was confirmed using Western blot assay. Cell death occured via the apoptosis pathway; however, the combination treatment significantly increased the apoptosis only for Mel IL/R cells. The enhanced cytotoxic effect was also associated with enhanced cell cycle arrest in the G0/G1 phase. Conclusion In general, we provide the evidence that dual inhibition of mTOR and MEK could be promising for further preclinical investigations.
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Affiliation(s)
- Oxana O Ryabaya
- Department of the Experimental Diagnostic and Tumor Therapy N.N., Bloknin National Medical Research Center of Oncology, 24 Kashirskoe Shosse, Moscow, 115478, Russia.
| | - Ivan S Abramov
- Center of Strategical Planning, Moscow, Russia, 10-1 Pogodinskaya Street, Moscow, 119121, Russia
| | - Dmitry A Khochenkov
- Department of the Experimental Diagnostic and Tumor Therapy N.N., Bloknin National Medical Research Center of Oncology, 24 Kashirskoe Shosse, Moscow, 115478, Russia.,Togliatti State University, Belorusskaya str. 14, Togliatti, 445020, Russia
| | - Roman Akasov
- Institute of Molecular Medicine Sechenov First Moscow State Medical University, 8-2 Trubetskaya Street, Moscow, 119991, Russia.,Department of Biomaterials and Biotechnologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Federal Scientific Research Center «Crystallography and Photonics», Russian Academy of Sciences, 17a Butlerova st, Moscow, 117997, Russia
| | - Nataly V Sholina
- Department of the Experimental Diagnostic and Tumor Therapy N.N., Bloknin National Medical Research Center of Oncology, 24 Kashirskoe Shosse, Moscow, 115478, Russia.,Institute of Molecular Medicine Sechenov First Moscow State Medical University, 8-2 Trubetskaya Street, Moscow, 119991, Russia
| | - Anastasia A Prokofieva
- Department of the Experimental Diagnostic and Tumor Therapy N.N., Bloknin National Medical Research Center of Oncology, 24 Kashirskoe Shosse, Moscow, 115478, Russia
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4
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Shershov VE, Ikonnikova AY, Vasiliskov VA, Lapa SA, Miftakhov RA, Kuznetsova VE, Chudinov AV, Nasedkina TV. The Efficiency of DNA Labeling with Near-Infrared Fluorescent Dyes. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920050188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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Abstract
ABSTRACT Specific alterations involving MAPK genes (MAP3K8 fusions, MAP3K3 fusions) have been recently detected in a subgroup of spitzoid neoplasms that seem to constitute a distinctive clinicopathologic group, occur mostly in younger patients (median age 18 years) and present with atypical histologic features associated with frequent homozygous deletion of CDKN2A, qualifying a high proportion of them as Spitz melanoma (malignant Spitz tumor). Apart from lesions with spitzoid morphology harboring MAP3K8 or MAP3K3 fusion, a single case with MAP2K1 deletion has been identified. The authors report herein 4 melanocytic lesions with a MAP2K1 mutation, all showing similar microscopic appearances, including spitzoid cytology and dysplastic architectural features, resembling so-called SPARK nevus, suggesting that these lesions may represent another distinctive group.
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Williams EA, Montesion M, Shah N, Sharaf R, Pavlick DC, Sokol ES, Alexander B, Venstrom J, Elvin JA, Ross JS, Williams KJ, Tse JY, Mochel MC. Melanoma with in-frame deletion of MAP2K1: a distinct molecular subtype of cutaneous melanoma mutually exclusive from BRAF, NRAS, and NF1 mutations. Mod Pathol 2020; 33:2397-2406. [PMID: 32483240 PMCID: PMC7685971 DOI: 10.1038/s41379-020-0581-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 11/12/2022]
Abstract
While the genomics of BRAF, NRAS, and other key genes influencing MAP kinase (MAPK) activity have been thoroughly characterized in melanoma, mutations in MAP2K1 (MEK1) have received significantly less attention and have consisted almost entirely of missense mutations considered secondary oncogenic drivers of melanoma. Here, we investigated melanomas with in-frame deletions of MAP2K1, alterations characterized as MAPK-activating in recent experimental models. Our case archive of clinical melanoma samples with comprehensive genomic profiling by a hybrid capture-based DNA sequencing platform was searched for MAP2K1 genetic alterations. Clinical data, pathology reports, and histopathology were reviewed for each case. From a cohort of 7119 advanced melanomas, 37 unique cases (0.5%) featured small in-frame deletions in MAP2K1. These included E102_I103del (n = 11 cases), P105_A106del (n = 8), Q58_E62del (n = 6), I103_K104del (n = 5), I99_K104del (n = 3), L98_I103del (n = 3), and E41_F53del (n = 1). All 37 were wild type for BRAF, NRAS, and NF1 genomic alterations ("triple wild-type"), representing 2.0% of triple wild-type melanomas overall (37/1882). Median age was 66 years and 49% were male. The majority arose from primary cutaneous sites (35/37; 95%) and demonstrated a UV signature when available (21/25; 84%). Tumor mutational burden was typical for cutaneous melanoma (median = 9.6 mut/Mb, range 0-35.7), and frequently mutated genes included TERTp (63%), CDKN2A (46%), TP53 (11%), PTEN (8%), APC (8%), and CTNNB1 (5%). Histopathology revealed a spectrum of appearances typical of melanoma. For comparison, we evaluated 221 cases with pathogenic missense single nucleotide variants in MAP2K1. The vast majority of melanomas with missense SNVs in MAP2K1 showed co-mutations in BRAF (58%), NF1 (23%), or NRAS (18%). In-frame deletions in MAP2K1, previously shown in experimental models to be strongly MAPK-activating, characterized a significant subset of triple wild-type melanoma (2.0%), suggesting a primary oncogenic role for these mutations. Comprehensive genomic profiling of melanomas enables detection of this alteration, which may have implications for potential therapeutic options.
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Affiliation(s)
- Erik A Williams
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA.
| | - Meagan Montesion
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Nikunj Shah
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Radwa Sharaf
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Dean C Pavlick
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Ethan S Sokol
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Brian Alexander
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Jeff Venstrom
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Julia A Elvin
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology, State University of New York Upstate Medical University, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Kevin Jon Williams
- Department of Physiology, Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Julie Y Tse
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology & Laboratory Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Mark C Mochel
- Departments of Pathology and Dermatology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
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7
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Emelyanova MA, Telysheva EN, Orlova KV, Ryabaya OO, Snigiryova GP, Abramov IS, Mikhailovich VM. Microarray-based analysis of the BRAF V600 mutations in circulating tumor DNA in melanoma patients. Cancer Genet 2020; 250-251:25-35. [PMID: 33249369 DOI: 10.1016/j.cancergen.2020.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/20/2020] [Accepted: 11/11/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) holds great potential for cancer therapy and can provide diagnostic and prognostic information before and during treatment. METHODS Plasma DNA samples from 97 melanoma patients, 20 healthy donors and 3 patients with benign skin tumors were analyzed by microarray analysis and droplet digital PCR (ddPCR). RESULTS A microarray for simultaneous detection of six BRAF V600 mutations in ctDNA has been developed. The method allows the detection of 0.05% mutated DNA from WT DNA background. For paired samples (pre-surgery plasma and tumor tissue) isolated from 74 patients, the concordance of genotypes between tumor DNA and ctDNA was 65% (48/74). BRAF mutations in ctDNA were detected in 27/50 patients with BRAF-positive tumors and in 3/24 patients with BRAF wild-type tumors. The presence of ctDNA BRAF mutations in 23 plasma samples from melanoma patients undergoing therapy correlated significantly with tumor progression (P=0.005). The increase in cell-free DNA levels measured by ddPCR also correlated with disease progression (P=0.02). The concordance of results obtained by microarray identification of BRAF mutations and those obtained by ddPCR was 91%. CONCLUSION The novel microarray-based approach can be a useful non-invasive tool for accurate identification of ctDNA BRAF mutations to monitor disease progression.
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Affiliation(s)
- Marina A Emelyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, 32 Vavilova St., Russian Federation
| | - Ekaterina N Telysheva
- Russian Scientific Center of Roentgen Radiology, Ministry of Healthcare of the Russian Federation, 117997 Moscow, Profsoyuznaya St. 86, Russian Federation
| | - Kristina V Orlova
- N.N. Blokhin National Medical Research Center for Oncology, Ministry of Health of the Russian Federation, 115478 Moscow, Kashirskoye shosse 24, Russian Federation
| | - Oxana O Ryabaya
- N.N. Blokhin National Medical Research Center for Oncology, Ministry of Health of the Russian Federation, 115478 Moscow, Kashirskoye shosse 24, Russian Federation
| | - Galina P Snigiryova
- Russian Scientific Center of Roentgen Radiology, Ministry of Healthcare of the Russian Federation, 117997 Moscow, Profsoyuznaya St. 86, Russian Federation
| | - Ivan S Abramov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, 32 Vavilova St., Russian Federation
| | - Vladimir M Mikhailovich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, 32 Vavilova St., Russian Federation.
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8
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Kerckhoffs KGP, Aallali T, Ambarus CA, Sigurdsson V, Jansen AML, Blokx WAM. Expanding spectrum of "spitzoid" lesions: a small series of 4 cases with MAP2K1 mutations. Virchows Arch 2020; 479:195-202. [PMID: 33040161 PMCID: PMC8298358 DOI: 10.1007/s00428-020-02940-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/10/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023]
Abstract
The molecular background of a significant proportion of spitzoid neoplasms is still unknown. Recently, activating mutations in MAP2K1 have been described in a few spitzoid lesions, but not in benign Spitz nevi. We report four cases of melanocytic tumors with spitzoid features in which a MAP2K1 mutation was detected. The lesions did not show a single distinct phenotype and ranged from benign to malignant. Two cases resembled desmoplastic Spitz nevi. Based on the combination of morphological, immunohistochemical, and molecular findings, one case was classified as benign, one as probably benign, possibly intermediate low-grade (MELTUMP—melanocytic tumor of unknown malignant potential), one case was classified as intermediate (MELTUMP), and one case was considered a superficial spreading melanoma with spitzoid features. Based on this, we conclude that MAP2K1 mutations can indicate a spitzoid genetic signature and can be found in both benign and malignant spitzoid neoplasms.
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Affiliation(s)
- K G P Kerckhoffs
- Department of Pathology, Maastricht University Medical Center+, Maastricht, The Netherlands.
| | - T Aallali
- Symbiant Pathology Expert Center, Hoorn/Zaandam, The Netherlands
| | - C A Ambarus
- Department of Pathology, Sint Antonius Hospital, Nieuwegein, The Netherlands
| | - V Sigurdsson
- Department of Dermatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A M L Jansen
- Department of Pathology, Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - W A M Blokx
- Department of Pathology, Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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9
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Ammour Y, Ryabaya O, Shchetinina Y, Prokofeva E, Gavrilova M, Khochenkov D, Vorobyev D, Faizuloev E, Shohin I, Zverev VV, Svitich O, Nasedkina T. The Susceptibility of Human Melanoma Cells to Infection with the Leningrad-16 Vaccine Strain of Measles Virus. Viruses 2020; 12:E173. [PMID: 32033013 PMCID: PMC7077263 DOI: 10.3390/v12020173] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/27/2020] [Accepted: 01/31/2020] [Indexed: 01/28/2023] Open
Abstract
Oncolytic viruses, including live attenuated measles virus (MV) vaccine strains, have recently been shown as promising therapeutic agents against human malignancies. In this study, the oncolytic potential of the attenuated vaccine strain Leningrad-16 (L-16) of MV was evaluated in a panel of human metastatic melanoma cell lines. The L-16 measles virus was shown to replicate within melanoma cells mediating direct cell killing of tumor cells, although all melanoma cell lines varied in regard to their ability to respond to L-16 MV infection, as revealed by the different pattern of the Interferon Stimulated Gene expression, cytokine release and mechanisms of cell death. Furthermore, the statistically significant L-16 measles virus related tumor growth inhibition was demonstrated in a melanoma xenograft model. Therefore, L-16 MV represents an appealing oncolytic platform for target delivery of therapeutic genes along with other attenuated measles virus strains.
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Affiliation(s)
- Yulia Ammour
- I.I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia; (Y.S.); (E.P.); (M.G.); (D.V.); (E.F.); (I.S.); (V.V.Z.); (O.S.)
| | - Oxana Ryabaya
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115478 Moscow, Russia; (O.R.); (D.K.)
| | - Yulia Shchetinina
- I.I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia; (Y.S.); (E.P.); (M.G.); (D.V.); (E.F.); (I.S.); (V.V.Z.); (O.S.)
| | - Elena Prokofeva
- I.I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia; (Y.S.); (E.P.); (M.G.); (D.V.); (E.F.); (I.S.); (V.V.Z.); (O.S.)
| | - Marina Gavrilova
- I.I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia; (Y.S.); (E.P.); (M.G.); (D.V.); (E.F.); (I.S.); (V.V.Z.); (O.S.)
| | - Dmitry Khochenkov
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115478 Moscow, Russia; (O.R.); (D.K.)
- Medicinal Chemistry Center, Togliatti State University, 445020 Togliatti, Russia
| | - Denis Vorobyev
- I.I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia; (Y.S.); (E.P.); (M.G.); (D.V.); (E.F.); (I.S.); (V.V.Z.); (O.S.)
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| | - Evgeny Faizuloev
- I.I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia; (Y.S.); (E.P.); (M.G.); (D.V.); (E.F.); (I.S.); (V.V.Z.); (O.S.)
| | - Igor Shohin
- I.I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia; (Y.S.); (E.P.); (M.G.); (D.V.); (E.F.); (I.S.); (V.V.Z.); (O.S.)
- Institute of biochemical technology and nanotechnology, RUDN University, 117198 Moscow, Russia
| | - Vitaly V. Zverev
- I.I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia; (Y.S.); (E.P.); (M.G.); (D.V.); (E.F.); (I.S.); (V.V.Z.); (O.S.)
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| | - Oxana Svitich
- I.I. Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia; (Y.S.); (E.P.); (M.G.); (D.V.); (E.F.); (I.S.); (V.V.Z.); (O.S.)
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 119146 Moscow, Russia
| | - Tatiana Nasedkina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 119991 Moscow, Russia;
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10
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Floristán A, Morales L, Hanniford D, Martinez C, Castellano-Sanz E, Dolgalev I, Ulloa-Morales A, Vega-Saenz de Miera E, Moran U, Darvishian F, Osman I, Kirchhoff T, Hernando E. Functional analysis of RPS27 mutations and expression in melanoma. Pigment Cell Melanoma Res 2019; 33:466-479. [PMID: 31663663 DOI: 10.1111/pcmr.12841] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/10/2019] [Accepted: 10/27/2019] [Indexed: 12/11/2022]
Abstract
Next-generation sequencing has enabled genetic and genomic characterization of melanoma to an unprecedent depth. However, the high mutational background plus the limited depth of coverage of whole-genome sequencing performed on cutaneous melanoma samples make the identification of novel driver mutations difficult. We sought to explore the somatic mutation portfolio in exonic and gene regulatory regions in human melanoma samples, for which we performed targeted sequencing of tumors and matched germline DNA samples from 89 melanoma patients, identifying known and novel recurrent mutations. Two recurrent mutations found in the RPS27 promoter associated with decreased RPS27 mRNA levels in vitro. Data mining and IHC analyses revealed a bimodal pattern of RPS27 expression in melanoma, with RPS27-low patients displaying worse prognosis. In vitro characterization of RPS27-high and RPS27-low melanoma cell lines, as well as loss-of-function experiments, demonstrated that high RPS27 status provides increased proliferative and invasive capacities, while low RPS27 confers survival advantage in low attachment and resistance to therapy. Additionally, we demonstrate that 10 other cancer types harbor bimodal RPS27 expression, and in those, similarly to melanoma, RPS27-low expression associates with worse clinical outcomes. RPS27 promoter mutation could thus represent a mechanism of gene expression modulation in melanoma patients, which may have prognostic and predictive implications.
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Affiliation(s)
- Alfredo Floristán
- Departments of Pathology, New York University School of Medicine, New York, NY, USA.,Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Leah Morales
- Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.,Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Douglas Hanniford
- Departments of Pathology, New York University School of Medicine, New York, NY, USA.,Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Carlos Martinez
- Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.,Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Elena Castellano-Sanz
- Departments of Pathology, New York University School of Medicine, New York, NY, USA.,Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Igor Dolgalev
- Applied Bioinformatics Laboratories, NYU Langone Health, New York, NY, USA
| | - Alejandro Ulloa-Morales
- Departments of Pathology, New York University School of Medicine, New York, NY, USA.,Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Eleazar Vega-Saenz de Miera
- Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.,Departments of Urology and Medicine, New York University School of Medicine, New York, NY, USA.,The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, USA
| | - Una Moran
- Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.,The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, USA
| | - Farbod Darvishian
- Departments of Pathology, New York University School of Medicine, New York, NY, USA.,Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Iman Osman
- Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.,Departments of Urology and Medicine, New York University School of Medicine, New York, NY, USA.,The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, USA
| | - Tomas Kirchhoff
- Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.,Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Eva Hernando
- Departments of Pathology, New York University School of Medicine, New York, NY, USA.,Interdisciplinary Melanoma Cooperative Group (IMCG), NYU Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
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Ikonnikova AY, Surzhikov SA, Pozhitnova VO, Zasedatelev AS, Nasedkina TV. 2'-O-Methyl Oligoribonucleotide Analogs Used to Change the Temperature Characteristics of Immobilized Probes and to Enhance the Specificity of Hybridization. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350918060118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Belysheva TS, Vishnevskaya YV, Nasedkina TV, Emelyanova MA, Abramov IS, Orlova KV, Lubchenko LN, Utyashev IA, Doroshenko MB, Demidov LV, Aliev MD. Melanoma arising in a Giant congenital melanocytic nevus: two case reports. Diagn Pathol 2019; 14:21. [PMID: 30782194 PMCID: PMC6381634 DOI: 10.1186/s13000-019-0797-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 02/10/2019] [Indexed: 12/22/2022] Open
Abstract
Background A giant congenital melanocytic nevus (GCMN) is found in 0.1% of live-born infants. If present, the lesion has a chance of about 6% to develop into malignant melanoma. Both children and adults can be affected by malignant melanoma arising in a giant congenital nevus. Up to 95% of GCMNs harbor NRAS mutations, and mutations in the BRAF, MC1R, TP53, and GNAQ genes have also been described. The individualization of therapy is required, but diagnostic and prognostic criteria remain controversial. Case presentations We report two cases: 1) melanoma arising in a giant congenital nevus during the first month of life complicated with neurocutaneous melanosis (NCM), and 2) melanoma arising in a giant congenital nevus during the first 6 months of life. Pathology, immunohistochemistry, and genetic analyses of tumor tissue were performed. The first case revealed only a non-pathogenic P72R polymorphism of the TP53 gene in the homozygote condition. For the second case, a Q61K mutation was detected in the NRAS gene. Conclusion Malignant melanoma associated with GCMN is rare and therefore poorly understood. Outcomes have been linked to the stage at diagnosis, but no additional pathological prognostic factors have been identified. The most frequent genetic event in giant CMNs is NRAS mutations, which was discovered in one of our cases. To accumulate evidence to improve disease prognosis and outcomes, children with congenital melanocytic nevus should be included in a systemic follow-up study from birth.
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Affiliation(s)
- Tatiana S Belysheva
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation
| | - Yana V Vishnevskaya
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation
| | - Tatiana V Nasedkina
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Marina A Emelyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ivan S Abramov
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kristina V Orlova
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation.
| | - Ludmila N Lubchenko
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation
| | - Igor A Utyashev
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation
| | - Marina B Doroshenko
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation
| | - Lev V Demidov
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation
| | - Mamed D Aliev
- Federal State Budgetary Institution, "N.N. Blokhin Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, 115478 Kashirskoye shosse, 24, Moscow, Russian Federation
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Ryabaya O, Prokofieva A, Akasov R, Khochenkov D, Emelyanova M, Burov S, Markvicheva E, Inshakov A, Stepanova E. Metformin increases antitumor activity of MEK inhibitor binimetinib in 2D and 3D models of human metastatic melanoma cells. Biomed Pharmacother 2018; 109:2548-2560. [PMID: 30551515 DOI: 10.1016/j.biopha.2018.11.109] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/02/2018] [Accepted: 11/25/2018] [Indexed: 12/29/2022] Open
Abstract
Melanoma is one of the most aggressive and treatment-resistant tumors that responsible for majority of skin-cancer related deaths. Here we propose a combination of MEK inhibitor binimetinib with metformin as a promising therapy against human melanoma cells in vitro, including BRAF -mutated A375, Mel Z, and Mel IL cells, and NRAS-mutated Mel MTP and Mel Me cells. Additionally, we obtained two close to clinical practice models of melanoma progression. The first one was vemurafenib-resistant Mel IL/R melanoma cells with acquired resistance to BRAF inhibition-targeted therapy, and the second one was tumor spheroids, which are 3D in vitro model of small-size solid tumors in vivo. The cytotoxicity of binimetinib and metformin was synergistic in both 2D and 3D melanoma culture and mediated through apoptotic pathway. The combination reduced the number of melanoma-formed colonies, inhibited cell invasion and migration, and led to G0/G1 cell cycle arrest through cyclin D/CDK4/CDK6 pathway. The mechanism of metformin and binimetinib synergy in melanoma cells was associated with increased activation of p-AMPKα and decreased p-ERK, but not with alterations in p-mTOR. In summary, the combination of metformin and binimetinib resulted in stronger anti-proliferative effects on melanoma cells compared to binimetinib alone, and therefore could be promising for clinical applications.
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Affiliation(s)
- Oxana Ryabaya
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
| | - Anastasia Prokofieva
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
| | - Roman Akasov
- Institute of Molecular Medicine Sechenov First Moscow State Medical University, 119991, 8-2 Trubetskaya street, Moscow, Russia; Cytomed J.S.Co, Russia; Federal Scientific Research Center «Crystallography and Photonics» Russian Academy of Sciences, 117997, 17a Butlerova st, Moscow, Russia.
| | - Dmitry Khochenkov
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
| | - Marina Emelyanova
- Department of Biological Microchips Engelhardt Institute of Molecular Biology, 119991, 32 Vavilova street, Moscow, Russia.
| | | | - Elena Markvicheva
- Department of Biomaterials and Biotechnologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Andrey Inshakov
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
| | - Evgenia Stepanova
- Department of Experimental Diagnostic and Tumor Therapy N.N. Blokhin National Medical Research Center for Oncology, 115478, 24 Kashirskoe shosse, Moscow, Russia.
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Gryadunov DA, Shaskolskiy BL, Nasedkina TV, Rubina AY, Zasedatelev AS. The EIMB Hydrogel Microarray Technology: Thirty Years Later. Acta Naturae 2018; 10:4-18. [PMID: 30713758 PMCID: PMC6351029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Indexed: 11/26/2022] Open
Abstract
Biological microarrays (biochips) are analytical tools that can be used to implement complex integrative genomic and proteomic approaches to the solution of problems of personalized medicine (e.g., patient examination in order to reveal the disease long before the manifestation of clinical symptoms, assess the severity of pathological or infectious processes, and choose a rational treatment). The efficiency of biochips is predicated on their ability to perform multiple parallel specific reactions and to allow one to study the interactions of biopolymer molecules, such as DNA, proteins, glycans, etc. One of the pioneers of microarray technology was the Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences (EIMB), with its suggestion to immobilize molecular probes in the three-dimensional structure of a hydrophilic gel. Since the first experiments on sequencing by hybridization on oligonucleotide microarrays conducted some 30 years ago, the hydrogel microarrays designed at the EIMB have come a long and successful way from basic research to clinical laboratory diagnostics. This review discusses the key aspects of hydrogel microarray technology and a number of state-ofthe-art approaches for a multiplex analysis of DNA and the protein biomarkers of socially significant diseases, including the molecular genetic, immunological, and epidemiological aspects of pathogenesis.
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Affiliation(s)
- D. A. Gryadunov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
| | - B. L. Shaskolskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
| | - T. V. Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
| | - A. Yu. Rubina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
| | - A. S. Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str., 32, Moscow, 119991, Russia
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