Integrative genomic, epigenetic, radiologic and histological characterization of pediatric glioneuronal tumors

par Mélanie Pages

Thèse de doctorat en Neurosciences

Sous la direction de Pascale Aubry épouse Varlet.

Soutenue le 06-11-2018

à Sorbonne Paris Cité , dans le cadre de École doctorale Cerveau, cognition, comportement (Paris) , en partenariat avec Université Paris Descartes (1970-2019) (établissement de préparation) .

Le président du jury était Dominique Figarella-Branger.

Le jury était composé de Pascale Aubry épouse Varlet, Dominique Figarella-Branger, Isabelle Salmon, Florence Pedeutour, Philippe Kahane, Rameen Beroukhim, Ahmed Idbaih.

Les rapporteurs étaient Isabelle Salmon, Florence Pedeutour.

mots clés

• Neurosciences
• Tumeurs cérébrales
• Tumeurs -- Classification
• Épigénétique
• Génomique

Titre traduit

Caractérisation intégrative radio-histologique, génomique et épigénétique des tumeurs glioneuronales pédiatriques

Résumé

Pas de résumé

mots clés

• Neuroscience

Résumé

The large-scale genomic studies performed recently has enabled the objective identification of numerous novel genomic alterations and highlighted that pediatric brain tumors often harbor quiet cancer genomes, with a single driver genomic alteration. This characteristic is of special interest in the current context of precision medicine development. Low-grade glioneuronal tumor group is highly heterogeneous and remains particularly challenging since it includes a broad spectrum of tumors, often poorly discriminated by their histopathological features and not completely molecularly characterized. We used targeted methods (IHC, FISH, targeted sequencing), and large scale genomic and epigenetic methodologies to perform an integrative analysis to further characterized papillary glioneuronal tumors (PGNT), midline gangliogliomas and dysembryoplastic neuroepithelial tumors (DNT). We demonstrated that PGNT is a distinct entity characterized by a PRKCA fusion. We highlighted that H3 K27M mutation can occur in association with BRAF V600E mutation in midline grade I glioneuronal tumors, showing that despite the presence of H3 K27M mutations, these cases should not be graded and treated as grade IV tumors because they have a better spontaneous outcome than classic diffuse midline H3 K27M-mutant glioma. The DNT study enable us 1) to specify that non-specific DNT corresponds to a clinico-histological tumor group encompassing diverse molecularly distinct entities and 2) to demonstrate that specific DNTs can be progressive tumors and harbored a distinct DNA methylation profile. Diagnosis and genomic profiling that can guide precision medicine require tissue acquisition by neurosurgical procedures that are often difficult or not possible. We validated a sample collection procedure and we developed methodologies to detect circulating tumor DNA (ctDNA) in CSF, plasma and urine to identify clinically relevant genomic alterations from a cohort of 235 pediatric patients with brain tumors. We optimized a method to process ctDNA and performed ultra-low pass whole genome sequencing (ULP-WGS) using unique molecular identifiers, confirming we can reliably construct sequencing libraries from CSF-, plasma- and urine-derived ctDNA. ULP-WGS has also been used to assess sequencing library quality, copy number variations (CNVs) and tumor fraction. The vast majority of samples undergoing ULPWGS exhibited no CNVs, consistent with either absence in the tumor or low levels of tumorderived cfDNA. To distinguish between these, we developed a hybrid capture sequencing panel allowing identification of specific mutations and fusions more common in pediatric brain tumors.