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Romanidou O, Apostolou P, Kouvelakis K, Tsangaras K, Eliades A, Achilleos A, Loizides C, Lemesios C, Ioannides M, Kypri E, Koumbaris G, Papadopoulou K, Papathanasiou A, Rigakos G, Xanthakis I, Fostira F, Kotoula V, Fountzilas G, Patsalis PC. Molecular profile and clinical features of patients with gliomas using a broad targeted next generation-sequencing panel. Oncol Lett 2022; 25:38. [PMID: 36589665 PMCID: PMC9773316 DOI: 10.3892/ol.2022.13624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/02/2022] [Indexed: 12/13/2022] Open
Abstract
Gliomas are the most common malignant primary brain tumors characterized by poor prognosis. The genotyping of tumors using next generation sequencing (NGS) platforms enables the identification of genetic alterations that constitute diagnostic, prognostic and predictive biomarkers. The present study investigated the molecular profile of 32 tumor samples from 32 patients with high-grade gliomas by implementing a broad 80-gene targeted NGS panel while reporting their clinicopathological characteristics and outcomes. Subsequently, 14 of 32 tumor specimens were also genotyped using a 55-gene NGS panel to validate the diagnostic accuracy and clinical utility of the extended panel. The median follow-up was 19.2 months. In total, 129 genetic alterations including 33 structural variants were identified in 38 distinct genes. Among 96 variants (single nucleotide variants and insertions and deletions), 38 were pathogenic and 58 variants of unknown clinical significance. TP53 was the most frequently mutated gene, followed by PTEN and IDH1 genes. Glioma patients with IDH1 mutant tumors were younger and had significantly longer overall survival compared to patients with wild-type IDH1 tumors. Similarly, tumors with TP53 mutations were more likely observed in younger patients with glioma. Subsequently, a comparison of mutational profiles of samples analyzed by both panels was also performed. Implementation of the comprehensive pan-cancer and the MOL panels resulted in the identification of 37 and 15 variants, respectively. Of those, 13 were common. Comprehensive pan-cancer panel identified 24 additional variants, 22 of which were located in regions that were not targeted by the MOL panel. By contrast, the MOL panel identified two additional variants. Overall, the present study demonstrated that using an extended tumor profile assay instead of a glioma-specific tumor profile panel identified additional genetic changes that may be taken into consideration as potential therapeutic targets for glioma diagnosis and molecular classification.
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Affiliation(s)
- Ourania Romanidou
- Department of Medicine, Medical Oncology Unit, Giannitsa General Hospital, 58100 Giannitsa, Greece
| | - Paraskevi Apostolou
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, 15341 Athens, Greece
| | - Kyriakos Kouvelakis
- Section of Biostatistics, Hellenic Cooperative Oncology Group, Data Office, 11526 Athens, Greece
| | | | | | | | | | | | | | - Elena Kypri
- NIPD Genetics Ltd., 2409 Nicosia, Republic of Cyprus
| | | | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece
| | - Athanasios Papathanasiou
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, 15341 Athens, Greece
| | - Georgios Rigakos
- Third Department of Medical Oncology, Hygeia Hospital, 15123 Athens, Greece
| | - Ioannis Xanthakis
- Oncology Department, European Interbalkan Medical Center, 55535 Thessaloniki, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, 15341 Athens, Greece
| | - Vassiliki Kotoula
- Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece,Aristotle University of Thessaloniki, 54006 Thessaloniki, Greece,Department of Medical Oncology, German Oncology Center, 4108 Limassol, Republic of Cyprus
| | - Philippos C. Patsalis
- NIPD Genetics Ltd., 2409 Nicosia, Republic of Cyprus,School of Medicine, University of Nicosia Medical School, 2417 Nicosia, Republic of Cyprus,Correspondence to: Professor Philippos C. Patsalis, NIPD Genetics Ltd., 31 Neas Engomis, Engomi, 2409 Nicosia, Republic of Cyprus, E-mail:
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Ducos B, Bensimon D, Scerbo P. Vertebrate Cell Differentiation, Evolution, and Diseases: The Vertebrate-Specific Developmental Potential Guardians VENTX/ NANOG and POU5/ OCT4 Enter the Stage. Cells 2022; 11:cells11152299. [PMID: 35892595 PMCID: PMC9331430 DOI: 10.3390/cells11152299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 01/02/2023] Open
Abstract
During vertebrate development, embryonic cells pass through a continuum of transitory pluripotent states that precede multi-lineage commitment and morphogenesis. Such states are referred to as “refractory/naïve” and “competent/formative” pluripotency. The molecular mechanisms maintaining refractory pluripotency or driving the transition to competent pluripotency, as well as the cues regulating multi-lineage commitment, are evolutionarily conserved. Vertebrate-specific “Developmental Potential Guardians” (vsDPGs; i.e., VENTX/NANOG, POU5/OCT4), together with MEK1 (MAP2K1), coordinate the pluripotency continuum, competence for multi-lineage commitment and morphogenesis in vivo. During neurulation, vsDPGs empower ectodermal cells of the neuro-epithelial border (NEB) with multipotency and ectomesenchyme potential through an “endogenous reprogramming” process, giving rise to the neural crest cells (NCCs). Furthermore, vsDPGs are expressed in undifferentiated-bipotent neuro-mesodermal progenitor cells (NMPs), which participate in posterior axis elongation and growth. Finally, vsDPGs are involved in carcinogenesis, whereby they confer selective advantage to cancer stem cells (CSCs) and therapeutic resistance. Intriguingly, the heterogenous distribution of vsDPGs in these cell types impact on cellular potential and features. Here, we summarize the findings about the role of vsDPGs during vertebrate development and their selective advantage in evolution. Our aim to present a holistic view regarding vsDPGs as facilitators of both cell plasticity/adaptability and morphological innovation/variation. Moreover, vsDPGs may also be at the heart of carcinogenesis by allowing malignant cells to escape from physiological constraints and surveillance mechanisms.
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Affiliation(s)
- Bertrand Ducos
- LPENS, PSL, CNRS, 24 rue Lhomond, 75005 Paris, France
- IBENS, PSL, CNRS, 46 rue d’Ulm, 75005 Paris, France
- High Throughput qPCR Core Facility, ENS, PSL, 46 rue d’Ulm, 75005 Paris, France
- Correspondence: (B.D.); (D.B.); (P.S.)
| | - David Bensimon
- LPENS, PSL, CNRS, 24 rue Lhomond, 75005 Paris, France
- IBENS, PSL, CNRS, 46 rue d’Ulm, 75005 Paris, France
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90094, USA
- Correspondence: (B.D.); (D.B.); (P.S.)
| | - Pierluigi Scerbo
- LPENS, PSL, CNRS, 24 rue Lhomond, 75005 Paris, France
- IBENS, PSL, CNRS, 46 rue d’Ulm, 75005 Paris, France
- Correspondence: (B.D.); (D.B.); (P.S.)
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