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

Author(s):Show less -

de Sousa, Graziella Ribeiro ^[1] ; Lira, Regia Caroline Peixoto ^{[2, 3]} ; de Almeida Magalhaes, Taciani ^{[4, 1]} ; da Silva, Keteryne Rodrigues ^[1] ; Nagano, Luis Fernando Peinado ^[1] ; Saggioro, Fabiano Pinto ^{[5, 6]} ; Baroni, Mirella ^[2] ; Marie, Suely Kazue Nagahashi ^[7] ; Oba-Shinjo, Sueli Mieko ^[7] ; Brandelise, Silvia ^[8] ; de Paula Queiroz, Rosane Gomes ^[2] ; Brassesco, Maria Sol ^[9] ; Scrideli, Carlos Alberto ^{[1, 2]} ; Tone, Luiz Gonzaga ^{[1, 2]} ; Valera, Elvis Terci ^[2]

Affiliation

^[1] Ribeirao Preto Med Sch, Dept Genet, 3900 Bandeirantes Ave, BR-14049900 Ribeirao Preto, SP - Brazil

^[2] Ribeirao Preto Med Sch, Dept Paediat, 3900 Bandeirantes Ave, BR-14049900 Ribeirao Preto, SP - Brazil

^[3] Univ Fed Triangulo Mineiro, Div Gen Pathol, Campus 1, Manuel Terra Sq, BR-38025200 Uberaba, MG - Brazil

^[4] Harvard Med Sch, Dept Cell Biol, Boston, MA 02115 - USA

^[5] Ribeirao Preto Med Sch, Dept Pathol, 3900 Bandeirantes Ave, BR-14049900 Ribeirao Preto, SP - Brazil

^[6] Rede DOr Sao Luiz Hosp, Dept Pathol, Rua Perobas, BR-04321120 Sao Paulo, SP - Brazil

^[7] Univ Sao Paulo, Fac Med FMUSP, Dept Neurol, Lab Cellular & Mol Biol, Sao Paulo, SP - Brazil

^[8] Boldrini Inst Ctr, Campinas, SP - Brazil

^[9] Univ Sao Paulo, Fac Philosophy Sci & Letters Ribeirao Preto, 3900 Bandeirantes Ave, BR-14040901 Ribeirao Preto, SP - Brazil

• Document type: Journal article
• Source: JOURNAL OF MOLECULAR MEDICINE-JMM; v. 99, n. 8, p. 1101-1113, AUG 2021.
• Web of Science Citations: 1

Abstract

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. (AU)

• FAPESP's process: 16/23972-6 - Molecular classification of pediatric ependymomas
• Grantee: Graziella Ribeiro de Sousa
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 14/20341-0 - Interactions between emerging therapeutic targets and developmental pathways associated with tumorigenesis: emphasis on pediatric malignancies
• Grantee: Luiz Gonzaga Tone
• Support Opportunities: Research Projects - Thematic Grants