Ganglioglioma with adverse clinical outcome and atypical histopathological features were defined by alterations in PTPN11/KRAS/NF1 and other RAS-/MAP-Kinase pathway genes

Acta Neuropathologica https://doi.org/10.1007/s00401-023-02561-5 ORIGINAL PAPER Ganglioglioma with adverse clinical outcome and atypical histopathological features were defined by alterations in PTPN11/ KRAS/NF1 and other RAS‑/MAP‑Kinase pathway genes Lucas Hoffmann1 · Roland Coras1 · Katja Kobow1 · Javier A. López‑Rivera2,3,4 · Dennis Lal3,4,5,6 · Costin Leu3,4,5,6 · Imad Najm4 · Peter Nürnberg6 · Jochen Herms7 · Patrick N. Harter7 · Christian G. Bien8 · Thilo Kalbhenn8,13 · Markus Müller8 · Tom Pieper9 · Till Hartlieb9 · Manfred Kudernatsch9 · Hajo Hamer10 · Sebastian Brandner11 · Karl Rössler11,12 · Ingmar Blümcke1 · Samir Jabari1 Received: 22 November 2022 / Revised: 27 February 2023 / Accepted: 9 March 2023 © The Author(s) 2023 Abstract Exome-wide sequencing studies recently described PTPN11 as a novel brain somatic epilepsy gene. In contrast, germline mutations of PTPN11 are known to cause Noonan syndrome, a multisystem disorder characterized by abnormal facial features, developmental delay, and sporadically, also brain tumors. Herein, we performed a deep phenotype-genotype analysis of a comprehensive series of ganglioglioma (GG) with brain somatic alterations of the PTPN11/KRAS/NF1 genes compared to GG with common MAP-Kinase signaling pathway alterations, i.e., BRAFV600E. Seventy-two GG were submitted to whole exome sequencing and genotyping and 84 low grade epilepsy associated tumors (LEAT) to DNA-methylation analysis. In 28 tumours, both analyses were available from the same sample. Clinical data were retrieved from hospital files including disease onset, age at surgery, brain localization, and seizure outcome. A comprehensive histopathology staining panel was available in all cases. We identified eight GG with PTPN11 alterations, copy number variant (CNV) gains of chromosome 12, and the commonality of additional CNV gains in NF1, KRAS, FGFR4 and RHEB, as well as BRAFV600E alterations. Histopathology revealed an atypical glio-neuronal phenotype with subarachnoidal tumor spread and large, pleomorphic, and multinuclear cellular features. Only three out of eight patients with GG and PTPN11/KRAS/NF1 alterations were free of disabling-seizures 2 years after surgery (38% had Engel I). This was remarkably different from our series of GG with only BRAFV600E mutations (85% had Engel I). Unsupervised cluster analysis of DNA methylation arrays separated these tumours from well-established LEAT categories. Our data point to a subgroup of GG with cellular atypia in glial and neuronal cell components, adverse postsurgical outcome, and genetically characterized by complex alterations in PTPN11 and other RAS-/MAP-Kinase and/or mTOR signaling pathways. These findings need prospective validation in clinical practice as they argue for an adaptation of the WHO grading system in developmental, glio-neuronal tumors associated with early onset focal epilepsy. Keywords Brain · Seizure · Summary plots · Epilepsy · DNA methylation Introduction Protein Tyrosine Phosphatase Non-receptor Type 11 (PTPN11) has been recently discovered as a new candidate gene in brain tissue obtained from drug-resistant structural epilepsies [2, 18, 23]. The PTPN11 gene encodes for an * Samir Jabari Extended author information available on the last page of the article early non-receptor-type protein tyrosine phosphatase SHP-2 (src homology region 2-domain phosphatase-2) of the RAS-/ MAP-Kinase pathway. Germline variants in PTPN11, e.g., missense variants or copy number variations (CNV), or other RAS-/MAP-Kinase signaling pathway genes including SHOC2, CBL, KRAS, are known to cause an autosomal dominant multisystem disorder—the Noonan syndrome— characterized by several non-central nervous system (CNS) disorders, including cardiovascular abnormalities, lymphatic abnormalities, and growth hormone deficiencies [10, 27, 30, 32]. Thirteen percent of patients with Noonan syndrome also 13 Vol.:(0123456789) Acta Neuropathologica have recurrent seizures and sporadically develop glial and glio-neuronal brain tumors, e.g., pilocytic astrocytoma and dysembryoplastic neuroepithelial tumors (DNT) [27, 30, 31]. We recently identified an accumulation of brain somatic PTPN11 alterations in low-grade epilepsy-associated brain tumors (LEAT) [23], the second largest lesion category in drug-resistant focal epilepsies amenable to neurosurgical treatment [6, 21]. Ganglioglioma (GG) account for approx. 64% of all LEAT, 82% of which affect the temporal lobe, and histopathologically classified as WHO CNS grade 1 [33]. 80% of these patients become free from disabling seizures, i.e., 5 years after surgery, with many patients also stopping their anti-seizure medication [21]. Nevertheless, no biomarker is available for the remaining 20% of patients who do not benefit from a tailored epilepsy surgery approach. We addressed this issue by studying a comprehensive cohort of GG with whole-exome sequencing, DNA methylation, histopathology, and clinical outcome parameter. Interestingly, our analysis identified a group of GG with complex alterations in PTPN11/KRAS/NF1 and other RAS-/MAPKinase or mTOR pathway genes, adverse clinical outcome, and atypical histopathological features. Methods One-hundred-twenty-eight samples of histopathologically confirmed LEAT and a pre-defined set of clinical features were collected at the University Hospital in Erlangen, Germany; Klinikum Bethel-Mara, Bielefeld University, Germany; and Schoen-Klinik Vogtareuth, Germany. Seventytwo samples were snap frozen at − 80 °C and submitted to whole-exome sequencing and Single-Nucleotide-Polymorphism analysis (SNP) using the Global Screening Array with Multi-disease drop-in (v1.0; Illumina, San Diego, CA, USA) as described elsewhere [23]. Eighty-four samples were formalin-fixed and paraffin-embedded (FFPE) and submitted to DNA methylation analysis using 450K and 850K arrays (Illumina, California, USA). Whole exome sequencing, SNP array, and DNA methylation analysis were jointly available in 28 samples (Table 1). The Ethics Committee of the Medical Faculty of the Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Germany, approved this study within the framework of the EU project “DESIRE” (FP7, grant agreement #602,531; AZ 92_14B) and European Reference Network EpiCARE” (grant agreement #769,051; AZ 193_18B). Histology and immunohistochemistry FFPE tissue blocks and glass slides were retrieved from the archives of the Neuropathological Institute at University 13 Hospital Erlangen. Hematoxylin and Eosin stainings were available from all blocks and microscopically examined by two senior authors and experienced neuropathologists (IB, RC). Additional immunohistochemical stainings were performed with the Ventana BenchMark ULTRA Immunostainer and the OptiView Universal DAB Detection Kit (Ventana Medical Systems, Tucson, AZ, USA) using the following panel of antibodies: Microtubule Associated Protein 2 (MAP2, clone C, mouse monoclonal, 1:100 dilution, Riederer (...truncated)