Dados do Trabalho

Título

NANOG and POU5F: Emerging Molecular Markers for Germinomas in Pediatric and Adult Germ Cell Tumors

Introdução

Germ cell tumors (GCTs) are a heterogeneous group of tumors that arise from primordial germ cells and occur in both pediatric and adult populations. While these tumors show similarities across age groups, clinical and histological differences warrant further investigation. Advancements in molecular profiling techniques have enabled researchers to delve deeper into the genetic landscape of GCTs, and transcriptomic analyses reveal unique gene expression patterns in pediatric and adult cases.

Objetivo

This study aimed to evaluate the expression of NANOG, POU5F, GATA6, HNF4A, FOXA2, and ERBB4 in pediatric and adult patients with GCTs using the nanopore sequencing methodology for pediatric cases and associate them with the data from Illumina sequencing of a publicly available cohort of adult GCTs.

Métodos

This study was approved by Institutional Review Board for Fundação Pio XII under the number 2367/2022. For pediatric analyses, five samples were selected including three dysgerminomas and two yolk sac tumors. Total RNA was extracted from frozen tumor tissue of pediatric GCTs collected at diagnosis and stored at Barretos Cancer Hospital Biobank with Qiasymphony. RNA-seq library was prepared using cDNA PCR barcoding, and sequencing was performed on MinION flow cell for up to 48h. Nanopore sequencing and data analyses were performed following standardized protocols developed by the University of North Carolina and Saint Jude Children’s Research Hospital researchers. The gene expression was normalized into a z-score and the heatmap was created using R Studio. For adult analyses, gene expression data from 149 patients were downloaded from the Testicular Germ Cell Tumors TCGA PanCancer study at cBioPortal.

Resultados

Pediatric data showed a clear separation of histological subtypes based on the gene expression profile, where NANOG and POU5F were highly expressed in dysgerminomas and GATA6, HNF4A, FOXA2, and ERBB4 were highly expressed in yolk sac tumors. In concordance, the cBioPortal cohort showed that the seminoma/embryonal carcinoma cluster also had a higher expression of NANOG and POU5F, although, the cluster with the higher expression of GATA6, HNF4A, FOXA2, and ERBB4 could not specify a histological subtype. The differential expression of those genes in germ cell tumors was described in past studies, but here we used a different sequencing methodology to associate our findings with data from the literature and other sequencing platforms.

Conclusões

Our results suggest that NANOG and POU5F could be molecular markers for germinomas. Furthermore, nanopore sequencing is a good technology for the classification of GCTs and could be used for the diagnosis of pediatric tumors since the Nanopore is cheaper, faster, and more friendly user compared to other platforms. Therefore, more studies with a higher number of pediatric samples are essential to validate these results.

Palavras-chave

Germ cell tumors, sequencing, nanopore, transcriptome, gene expression

Financiador do resumo

FAPESP, Saint Jude Children’s Research Hospital, Barretos Cancer Hospital