Duplications of KIAA1549 and BRAF screening by Droplet Digital PCR from formalin-fixed paraffin-embedded DNA is an accurate alternative for KIAA1549-BRAF fusion detection in pilocytic astrocytomas

Pilocytic astrocytomas represent the most common glioma subtype in young patients and account for 5.4% of all gliomas. They are characterized by alterations in the RAS–MAP kinase pathway, the most frequent being a tandem duplication on chromosome 7q34 involving the BRAF gene, resulting in oncogenic BRAF fusion proteins. BRAF fusion involving the KIAA1549 gene is a hallmark of pilocytic astrocytoma, but it has also been recorded in rare cases of gangliogliomas, 1p/19q co-deleted oligodendroglial tumors, and it is also a common feature of disseminated oligodendroglial-like leptomeningeal neoplasm. In some difficult cases, evidence for KIAA1549-BRAF fusion is of utmost importance for the diagnosis. Moreover, because the KIAA1549-BRAF fusion constitutively activates the MAP kinase pathway, it represents a target for drugs such as MEK inhibitors, and therefore, the detection of this genetic abnormality is highly relevant in the context of clinical trials applying such new approaches. In the present study, we aimed to use the high sensitivity of Droplet Digital PCR (DDPCR™) to predict KIAA1549-BRAF fusion on very small amounts of formalin-fixed paraffin-embedded tissue in routine practice. Therefore, we analyzed a training cohort of 55 pilocytic astrocytomas in which the KIAA1549-BRAF fusion status was known by RNA sequencing used as our gold standard technique. Then, we analyzed a prospective cohort of 40 pilocytic astrocytomas, 27 neuroepithelial tumors remaining difficult to classify (pilocytic astrocytoma versus ganglioglioma or diffuse glioma), 15 dysembryoplastic neuroepithelial tumors, and 18 gangliogliomas. We could demonstrate the usefulness and high accuracy (100% sensitivity and specificity when compared to RNA sequencing) of DDPCR™ to assess the KIAA1549-BRAF fusion from very low amounts of DNA isolated from formalin-fixed paraffin-embedded specimens. BRAF duplication is both necessary and sufficient to predict this fusion in most cases and we propose that this single analysis could be used in routine practice to save time, money, and precious tissue

Molecular caracteristics of low grade pediatric brain tumors

La classification OMS des tumeurs cérébrales de l'enfant distingue les tumeurs gliales des tumeurs glioneuronales, les gliomes circonscrits des infiltrants. Elle représente le meilleur indicateur pronostic mais se heurte pourtant à des limites de reproductibilité. Pour mieux préciser le diagnostic, mieux définir des sous-groupes de pronostic différent, et mieux orienter le thérapeutique, nous avons recherché les profils moléculaires de 108 tumeurs cérébrales circonscrites de l'enfant : astrocytome pilocytique (PA), tumeurs neuroépithéliales dysembryoplasiques (DNT), xanthoastrocytomes pléïomorphes (PXA) et gangliogliomes (GG). Aucune différence n'est retrouvée entre les gliomes corticaux de grade II (GC) et les DNT concernant IDH1 et 2, TP53 et la délétion1p19q. Les DNT non spécifiques et les GC partagent le même profil incluant CD34 et la mutation V600E de BRAF dans 50% des cas. Le PXA exprime la mutation V600E de BRAF dans plus de 50 % des cas et se rapproche du groupe des tumeurs glioneuronales. Concernant le PA, nous confirmons le caractère péjoratif de la topographie hypothalamo-chiasmatique, de l'histologie pilomyxoide, de l'âge inférieur à 36 mois et de l'exérèse partielle. A l'opposé des tumeurs infiltrantes qui appartiendraient au groupe " histones dépendantes", les tumeurs circonscrites pourraient être regroupées sous le terme "MAPKinases dépendantes". On y distinguerait alors les tumeurs avec fusion KIAA1543-BRAF de celles avec mutation V600E de BRAF. Ce travail a permis de mieux caractériser les tumeurs gliales et glioneuronales de l'enfant, reposant sur le transfert en routine de marqueurs moléculaires simples.The OMS classification for pediatric brain tumors includes glial tumors and mixed glial and glioneuronal tumors, diffuse and no diffuse glioma. All strategic decision making are based on this current classification but it drives to some limits of diagnosis reproductibility.The goal of our study was to define molecular profils for low grade no diffuse pediatric brain tumors including pilocytic astrocytoma (PA), dysembryoplasic neuroepithelial tumor (DNT), pleiomorphic xanthoastrocytoma (PXA) and benign gangliogliome (GG), to improve the quality of diagnosis, define different subgroups with different prognosis and then to improve treatment strategy decision making.No molecular difference was found between cortical grade II glioma (GC) and DNT regarding IDH1 and 2 TP53 alterations and 1p19q deletion. Similarly 50 % of no specific form of DNT share the same molecular profil with GC with CD34 expression and V600E mutation of BRAF. PXA demonstrated BRAFV600E mutation in 60 % of cases. PXA could then be very close glioneuronal tumors. Finally in PA we confirmed the negative impact of hypothalochiasmatic location, pilomyxoid diagnosis and age lower than 36 months and partial resection. We could work on the elaboration of a new classification and define the group named “Histone dependant” for tumors with histone aberrations and the group named “MAPKinases dependant” for tumors with either KIAA 1543-BRAF fusion or V600E BRAF mutation.In conclusion, this work has led to improve the molecular profil characteristics of glioneuronal tumors of childhood with different easy diagnostic markers that can be used in routine practice, and could potentially replace DNA sequencing

Secondes tumeurs après traitement d'un cancer de l'enfant (à propos de 844 patients traités au Centre Léon Bérard [de Lyon] entre 1975 et 1985)

LYON1-BU Santé (693882101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Droplet digital PCR is a powerful technique to demonstrate frequent <i>FGFR1</i> duplication in dysembryoplastic neuroepithelial tumors

International audienceDysembryoplastic neuroepithelial tumors (DNT) share V600E mutation in the BRAF gene with other low grade neuroepithelial tumors (LGNTs). FGFR1 internal tandem duplication of the tyrosine-kinase domain (FGFR1-ITD), another genetic alteration that also leads to MAP kinase pathway alteration, has been previously reported in LGNTs by whole-genome sequencing. In the present study we searched for FGFR1-ITD by droplet digital PCR (DDPCR™) and for FGFR1 point mutations by HRM-sequencing in a series of formalin-fixed paraffin-embedded (FFPE) LGNTs including 12 DNT, 2 oligodendrogliomas lacking IDH mutation and 1p/19q co-deletion (pediatric-type oligodendrogliomas; PTOs), 3 pediatric diffuse astrocytomas (PDAs), 14 gangliogliomas (GGs) and 5 pilocytic astrocytomas (PAs). We showed by DDPCR™ that 5/12 DNT, but none of the other LGNTs, demonstrated FGFR1-ITD. In addition, these cases also accumulated phosphorylated-FGFR1 protein as shown by immunohistochemistry. FGFR1 G539R point mutation was only recorded in one DNT that also showed FGFR1-ITD. Interestingly, these FGFR1 alterations were mutually exclusive from BRAF V600E mutation that was recorded in 13 LGNTs (3 DNTs, 1 PTO, 2 PDAs, 5 GGs and 2 PAs). Therefore, FGFR1 alteration mainly represented by FGFR1-ITD is a frequent event in DNT. DDPCR™ is an easy and alternative method than whole-genome sequencing to detect FGFR1-ITD in FFPE brain tumors, in routine practice