Clinical value of chromosome arms 19q and 11p losses in low-grade gliomas

Neuro-Oncology Clinical value of chromosome arms 19q and 11p losses in low-grade gliomas Agust Alentorn 0 Hinke F. van Thuijl 0 Yannick Marie 0 Hussa Alshehhi 0 Catherine Carpentier 0 Blandine Boisselier 0 Florence Laigle-Donadey 0 Karima Mokhtari 0 Ilari Scheinin 0 Pieter Wesseling 0 Bauke Ylstra 0 Laurent Capelle 0 Khe Hoang-Xuan 0 Marc Sanson 0 Jean-Yves Delattre 0 Jaap C. Reijneveld 0 Ahmed Idbaih () 0 0 Centre de Recherche de l'Institut du Cerveau et de la Moelle Epinie`re (CRICM), UMRS 975, Inserm U 975, CNRS, UMR 7225, Universite Pierre et Marie Curie , Paris, France (A.A., Y.M, C.C., B.B., K.M., K.H.-X., M.S., J.-Y.D. , A.I.); Department of Neuropathology (H.A., K.M.); Department of Neurology 2-Mazarin (F.L.-D., K.H.-X. , M.S., J.-Y.D. , A.I.); Department of Neurosurgery, AP-HP, Groupe Hospitalier Pitie -Salpetrie re , Paris , France ( L.C.); Department of Neurology (H.F.v.T., J.C.R.); Department of Pathology, VU University Medical Center , Amsterdam , The Netherlands (I.S., P.W. , B.Y.); Department of Pathology, Radboud University Nijmegen Medical Centre , Nijmegen , The Netherlands (P.W.) Background. Diffuse low-grade gliomas (LGGs) form a heterogeneous subgroup of gliomas in adults. Chromosome (chr) arms 1p/19q codeletion and IDH mutation have been shown to be closely associated with oligodendroglial phenotype and better prognosis. We sought to identify relevant biomarkers in non 1p/19q codeleted LGGs. Methods. We characterized a retrospective series of 126 LGGs using genomic arrays, microsatellite analysis, IDH sequencing, MGMT promoter methylation assay, and p53 expression analysis. Results. Our study confirms that 1p/19q codeletion, mutually exclusive with p53 overexpression, was associated with: (i) better prognosis, (ii) oligodendroglial phenotype, (iii) MGMT promoter methylation, and (iv) IDH mutation. Interestingly, 1p/19q codeleted tumors occur in older patients at diagnosis. Our study shows that non 1p/19q codeleted LGGs can be divided in 5 main genomic subgroups: (i) 11p loss, (ii) 19q loss (iii) 7 gain, (iv) 19 gain, and (v) unclassified. In non 1p/19q codeleted LGGs, we demonstrated that (i) 11p loss is associated with astrocytoma phenotype and has an independent negative prognostic value, and (ii) 19q loss diminished the favorable prognostic value of IDH mutation. Our findings were validated in an independent cohort of 98 LGGs. Conclusion. Novel genomic entities and biomarkers have been identified in non 1p/19q codeleted LGGs. Our findings may help to stratify non 1p/19q codeleted LGGs, facilitating future individualization of treatment. Further prospective studies are warranted to support our findings. Diffuse low-grade gliomas (LGGs, WHO grade II) in adults form a Over the past decades, several molecular markers with clinical very heterogeneous group of neoplasms in terms of pathological relevance have been identified in LGGs. They might help to establish and clinical features.1,2 They include diffuse WHO grade II astrocy- a histomolecular classification of LGGs:6 - 8 (i) chr arms 1p/19q tomas, oligodendrogliomas, and oligoastrocytomas. Most often, codeletion;6,9,10 (ii) isocitrate dehydrogenase (IDH) 1 and 2 mutaLGGs are slow growing tumors. However, they inevitably recur tions,8,10,11 (iii) TP53 mutation/p53 overexpression,11,12 and (iv) and progress to higher-grade tumors (ie, anaplastic gliomas/ MGMT promoter methylation.13,14 Non 1p/19q codeleted LGGs WHO grade III and glioblastomas/WHO grade IV).2,3 The current have not been perfectly characterized so far but their characterizaclassification of LGGs is based on morphological criteria edited by tion is likely to include several genomic groups. Triple-negative the WHO.2 In practice, diagnosis of LGGs remains challenging, tumors (ie, without p53 overexpression, 1p/19q codeletion, and with significant intra- and interobserver variability.4 In addition, IDH mutation) have recently been described as a tumor group these tumors have a broad range of survival that varies from 1 with worse prognosis.12,15 In order to decipher non 1p/19q codeto 30 years.5 leted LGGs at a molecular level, we performed a genome-wide biomarker; genomic array; low-grade gliomas; IDH; MGMT; TP53 - analysis in a cohort of 126 LGGs and validated our results in an independent cohort of 98 samples. Material and Methods Patients and Tumors The following criteria were used to include cases and tumors in the present study: (i) aged 18 years or older at pathological diagnosis, (ii) diagnosis of supratentorial LGG (astrocytoma, oligodendroglioma, or oligoastrocytoma) according to the WHO classification at first surgery,2 (iii) detailed clinical information at diagnosis and during follow-up, (iv) availability of paired blood and fresh frozen tumor samples, (v) informed consent from participants for molecular analysis, and (vi) genomic profiling of the tumor DNA by bacterial artificial chromosome (BAC)-array based comparative genomic hybridization (BAC-aCGH). All tumors were centrally reviewed by 2 neuropathologists (K.M. and H.A.), who were blinded for molecular and clinical data. All patients received conventional therapy consisting of surgical resection as extensive as clinically and technically possible. Surgery was followed by radiotherapy and/or alkylating-based chemotherapy (nitrosourea or temozolomide) at unequivocal clinical and/or radiological tumor progression. DNA Extraction and BAC-aCGH DNA extraction was performed using DNeasy Mini kit (Qiagen) according to the manufacturers recommendations. DNA concentration and quality were determined by spectrophotometry (NanoDropw). All samples had high-quality genomic DNA with an A260-A280 ratio purity of 1.8:2. Onemegabase resolution BAC-aCGH experiments were conducted as described previously.16 MGMT Promoter Methylation Analysis The EZ DNA Methylation Gold Kit (Zymo Research) for bisulfite conversion of DNA was used for epigenomic analyses. Starting amount of DNA was 300 ng, and all modification reactions were performed according to manufacturers instructions. PCR amplification and high-resolution melting analysis were carried out in LighCycler480 (Rochew) using the following primer sequences: 5-CGTTTGCGATTTGGTGAGTGTT-3 and 5-CCTACAAAA CCACTCGAAACTACCA-3. Amplification consisted of 10 minutes at 958C, followed by 50 cycles of 15 seconds at 958C, 30 seconds at 608C, and 30 seconds at 728C. After amplification, a postamplification melting curve program was initiated by heating to 958C for 1 minute, cooling to 708C for 30 seconds, and increasing the temperature to 958C (heating rate 0.018C/s) while continuously measuring fluorescence. Artificial methylation using CpG Methylase M.ssI M0226S (New England Biolabsw) was performed according manufacturers instructions and used as a positive control. Peripheral blood DNA was considered negative control. When the peak corresponding to methylated DNA was .50% of the corresponding unmethylated DNA peak, the sample was considered (...truncated)