A coordinated approach for the assessment of molecular subgroups in pediatric ependymomas using low-cost methods.

Autor: de Sousa GR; Department of Genetics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil. graziellasousa@usp.br., Lira RCP; Department of Paediatrics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil.; Division of General Pathology, Federal University of Triângulo Mineiro, Campus I, Manuel Terra square, Uberaba, Minas Gerais, 38025-200, Brazil., de Almeida Magalhães T; Department of Genetics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil.; Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA., da Silva KR; Department of Genetics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil., Nagano LFP; Department of Genetics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil., Saggioro FP; Department of Pathology, Ribeirão Preto Medical School, Ribeirão Preto, 3900 Bandeirantes Avenue, SP, 14049-900, Brazil.; Department of Pathology, Rede D'Or São Luiz Hospital, São Paulo, Rua das Perobas, SP, 04321-120, Brazil., Baroni M; Department of Paediatrics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil., Marie SKN; Laboratory of Cellular and Molecular Biology, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, SP, Brazil., Oba-Shinjo SM; Laboratory of Cellular and Molecular Biology, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, SP, Brazil., Brandelise S; Boldrini Institute Center , Campinas, SP, Brazil., de Paula Queiroz RG; Department of Paediatrics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil., Brassesco MS; Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, 3900 Bandeirantes Avenue, SP, 14040-901, Brazil., Scrideli CA; Department of Genetics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil.; Department of Paediatrics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil., Tone LG; Department of Genetics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil.; Department of Paediatrics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil., Valera ET; Department of Paediatrics, Ribeirão Preto Medical School, 3900 Bandeirantes Avenue, Ribeirão Preto, SP, 14049-900, Brazil.
Jazyk: angličtina
Zdroj: Journal of molecular medicine (Berlin, Germany) [J Mol Med (Berl)] 2021 Aug; Vol. 99 (8), pp. 1101-1113. Date of Electronic Publication: 2021 Apr 26.
DOI: 10.1007/s00109-021-02074-2
Abstrakt: Although ependymoma (EPN) molecular subgroups have been well established by integrated high-throughput platforms, low- and middle-income countries still need low-cost techniques to promptly classify these molecular subtypes. Here, we applied low-cost methods to classify EPNs from a Brazilian cohort with 60 pediatric EPN patients. Fusion transcripts (C11orf95-RELA, YAP1-MAMLD1, and YAP1-FAM118B) were investigated in supratentorial EPN (ST-EPNs) samples through RT-PCR/Sanger sequencing and immunohistochemistry (IHC) for p65/L1CAM. qRT-PCR and IHC were used to evaluate expression profiling of CXorf67, LAMA2, NELL2, and H3K27me3 in posterior fossa EPN (PF-EPNs) samples. In silico analysis was performed using public microarray data to validate the molecular assignment PF-EPNs with LAMA2/NELL2 markers. RELA cases and YAP1-MAMLD1 fusions were identified in nine and four ST-EPNs, respectively. An additional RELA case was identified by IHC. Of note, LAMA2 and NELL2 gene expression and immunoprofiling were less accurate for classifying PF-EPNs, which were confirmed by in silico analysis. Yet, H3K27me3 staining was sufficient to classify PF-EPN subgroups. Our results emphasize the feasibility of a simplified strategy to molecularly classify EPNs in the vast majority of cases (49/60; 81.7%). A coordinated combination of simple methods can be effective to screen pediatric EPN with the available laboratory resources at most low-/mid-income countries, giving support for clinical practice in pediatric EPN. KEY MESSAGES: Low- and middle-income countries need effective low-cost approaches to promptly distinguish between EPN molecular subgroups. RT-PCR plus Sanger sequencing is able to recognize the most common types of RELA and YAP1 fusion transcripts in ST-EPNs. Genetic and protein expressions of LAMA2 and NELL2 are of limited value to accurately stratify PF-EPNs. Immunohistochemical staining for H3K27me3 may be used as a robust method to accurately diagnose PF-EPNs subgroups. A coordinated flow diagram based on these validated low-cost methods is proposed to help clinical-decision making and to reduce costs with NGS assessment outside research protocols.
(© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
Databáze: MEDLINE
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