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Molecular Diagnosis of Diffuse Gliomas Through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid

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Molecular Diagnosis of Diffuse Gliomas Through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid Published OnlineFirst April 3, 2018; DOI: 10.1158/1078-0432.CCR-17-3800 Personalized Medicine and Imaging Clinical Cancer Research Molecular Diagnosis of Diffuse Gliomas through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid Francisco Martínez-Ricarte1,2,3, Regina Mayor1, Elena Martínez-Saez 2, Carlota Rubio-Perez 4, Estela Pineda5, Esteban Cordero2, Marta Cicuendez 2, Maria A. Poca2,3, Nuria Lopez-Bigas 4, Santiago Ramon y Cajal2,6, María Vieito1, Joan Carles1, Josep Tabernero1,6, Ana Vivancos1, Soledad Gallego2, Francesc Graus5, Juan Sahuquillo2,3, and Joan Seoane1,3,6,7 Abstract Background: Diffuse gliomas are the most common pri- patients and performed a histopathologic characterization of mary tumor of the brain and include different subtypes with the tumors. diverse prognosis. The genomic characterization of diffuse Results: Analysis of the mutational status of the IDH1, IDH2, gliomas facilitates their molecular diagnosis. The anatomical TP53, TERT, ATRX, H3F3A, and HIST1H3B genes allowed localization of diffuse gliomas complicates access to tumor the classification of 79% of the 648 diffuse gliomas analyzed, specimens for diagnosis, in some cases incurring high-risk into IDH-wild-type glioblastoma, IDH-mutant glioblastoma/ surgical procedures and stereotactic biopsies. Recently, diffuse astrocytoma and oligodendroglioma, each subtype exhi- cell-free circulating tumor DNA (ctDNA) has been identified biting diverse median overall survival (1.1, 6.7, and 11.2 years, in the cerebrospinal fluid (CSF) of patients with brain respectively). We developed a sequencing platform to simulta- malignancies. neously and rapidly genotype these seven genes in CSF ctDNA Patients and Methods: We performed an analysis of IDH1, allowing the subclassification of diffuse gliomas. IDH2, TP53, TERT, ATRX, H3F3A, and HIST1H3B gene mutations Conclusions: The genomic analysis of IDH1, IDH2, TP53, in two tumor cohorts from The Cancer Genome Atlas (TCGA) ATRX, TERT, H3F3A, and HIST1H3B gene mutations in CSF including 648 diffuse gliomas. We also performed targeted exome ctDNA facilitates the diagnosis of diffuse gliomas in a timely sequencing and droplet digital PCR (ddPCR) analysis of these manner to support the surgical and clinical management of these seven genes in 20 clinical tumor specimens and CSF from glioma patients. Clin Cancer Res; 1–8. Ó2018 AACR. Introduction overall survival. Grade IV glioma, GBM, is one of the most aggressive tumors with less than 10% of patients surviving Diffuse gliomas are the most frequent primary malignant beyond 5 years (3). Magnetic resonance imaging (MRI) is the tumors of the central nervous system (CNS) and include IDH- principal imaging modality for patients with suspected brain wild-type glioblastoma multiforme (GBM), IDH-mutant GBM, lesions but for a definitive diagnosis, tumor tissue (from biopsy diffuse astrocytomas, anaplastic astrocytomas, oligodendro- or surgical resection) is required (4–6). gliomas, anaplastic oligodendroglioma, and diffuse midline Genomic characterization of tumors is crucial for optimal gliomas (1, 2). Diffuse gliomas exhibit a wide range of prog- diagnosis and treatment. However, characterization of cancer nosis depending on the grade, from 1 to 15 years median is challenged by evolving intratumor heterogeneity, which requires thorough and continuous analysis of genomic com- plexity over time. This is particularly relevant in brain malig- 1Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain. 2Vall d'Hebron nancies where the genomic landscape changes in response to Institut de Recerca (VHIR), Vall d'Hebron University Hospital, Barcelona, Spain. treatment or during relapse (7, 8). However, availability of 3Universitat Autonoma de Barcelona, Cerdanyola del Valles, Spain. 4Institut de glioma samples for characterization and correct diagnosis can 5 Recerca Biomedica (IRB), Barcelona, Spain. Hospital Clinic, University of be challenging. The anatomical location of gliomas can com- Barcelona and Institut d'Investigacio Biomedica August Pi i Sunyer (IDIBAPS), plicate tumor access, incurring high-risk surgical procedures and Barcelona, Spain. 6CIBERONC, Barcelona, Spain. 7Institucio Catalana de Recerca i Estudis Avancats¸ (ICREA), Barcelona, Spain. stereotactic biopsies. Moreover, specimens may be small and not representative, hampering correct diagnosis or even neces- F. Martínez-Ricarte and R. Mayor contributed equally to this article. sitating multiple surgical samplings to clarify final pathologic Corresponding Author: Joan Seoane, Vall d'Hebron Institute of Oncology, diagnosis. In addition, the surgical intervention strategy and c/Natzaret, 115-117, 08035 Barcelona, Spain. Phone: 34-93-254-34-50; E-mail: assessment of the surgical risk–benefit balance depend on the jseoane@vhio.net glioma subtype (1, 9–11). This implies that an intraoperative doi: 10.1158/1078-0432.CCR-17-3800 histologic diagnosis may be required, possibly delaying the Ó2018 American Association for Cancer Research. surgical procedure. Repeat surgical interventions may be needed www.aacrjournals.org OF1 Downloaded from clincancerres.aacrjournals.org on September 30, 2021. © 2018 American Association for Cancer Research. Published OnlineFirst April 3, 2018; DOI: 10.1158/1078-0432.CCR-17-3800 Martínez-Ricarte et al. plementary Fig. S1) and diagnosed by histologic analysis. All Translational Relevance patients underwent surgical resection, and CSF was collected Diffuse gliomas include different subtypes with diverse prior to surgery by lumbar puncture, except for two samples prognosis ranging from 1 to 15 years median overall survival. obtained from the cisterna magna during a warm autopsy proce- Thus, the classification of this type of tumors is crucial for the dure, and one sample from the brain ventricle through a cerebral correct clinical and surgical managing of patients. Recent shunt. The study was approved by the local ethics committee, and advances show that the genomic characterization of diffuse written informed consent was obtained from all patients. gliomas facilitates their molecular diagnosis. However, the anatomical localization of diffuse gliomas complicates access DNA extraction to tumor specimens for diagnosis, in some cases incurring DNA from fresh tumor tissue samples was extracted using the high-risk surgical procedures. Recently, ctDNA has been iden- QIAamp DNA micro kit (Qiagen), and germline DNA from fi ti ed in the CSF of patients with brain malignancies. We have peripheral blood lymphocytes was extracted using the QIAamp developed a sequencing platform to simultaneously and rap- DNA blood mini kit. For formalin-fixed paraffin-embedded —IDH1, IDH2, TP53, ATRX, TERT, idly genotype seven genes tumor samples, five 10-mm sections were obtained from the H3F3A, HIST1H3B— and in CSF ctDNA allowing the sub- previously selected tumoral area and processed using the QIAamp fi classi cation of diffuse gliomas. Our results show that CSF DNA FFPE tissue kit. CSF-derived ctDNA was extracted using the ctDNA can be used as a liquid biopsy to diagnose diffuse QIAamp Circulating Nucleic Acids kit and quantified using a gliomas, avoiding risky surgical procedures and leading to a Qubit Fluorometer. better management of CNS malignancies. Mutational analysis by amplicon sequencing and ddPCR DNA from matched glioma tumor tissue, peripheral blood, and CSF samples underwent custom amplicon sequencing, to clarify tumor pseudoprogression on treatment or confirm targeting all exons of IDH1, IDH2, ATRX, and TP53. In brief, early relapses. Taken together, a relatively noninvasive method DNA libraries were prepared using the Nebnext Library Prep for brain tumor characterization to facilitate molecular diagno- kit for Illumina, and paired-end 100-bp reads were generated sis would greatly assist the management of diffuse gliomas, on the Illumina Hiseq2500. Reads were aligned to the reference minimizing complex and high-risk surgical procedures. human genome hg19 using the Burrows-Wheeler Aligner During the past decade, large-scale DNA sequencing efforts v.07.12. Somatic variants were called using VarScan2, and only have identified key genomic alterations across glioma subtypes, mutations with VarScan2 P < 0.05, total coverage 10 reads, facilitating classification (12–15). Recently, the 2016 CNS WHO variant coverage 7 reads, and with allelic frequencies >5%, proposed the integration of histology and genetic analyses to were considered. All candidate mutations were reviewed define glioma entities. Diffuse gliomas can be subdivided by the manually using the Integrative Genomics Viewer. presence of IDH mutations, and within the subgroup of Genomic DNA (10 ng) from tumor tissues, and germline DNA IDH-mutant gliomas the presence of codeletions of the 1p/19q from peripheral blood lymphocytes, and CSF DNA (2–5 ng) from chromosome arms as well as mutations of the TERT gene pro- the same patient were used for digital PCR analysis, using the moter ATRX and/or TP53 distinguish between diffuse astro- QX200 Droplet Digital PCR system per the manufacturer's pro- cytomas and oligodendrogliomas (12, 13, 16). Moreover, diffuse tocols and the literature (21). Custom Taqman SNP genotyping midline gliomas are characterized by mutations in the H3F3A and assays for ddPCR were designed to detect IDH1, IDH2, TP53, HIST1H3B genes (17). Importantly, these tumors are usually H3F3A K27M, and HIST1H3B K27M point mutations and the located in the brain stem, thalamus, and spinal cord, making corresponding wild-type alleles. Two ddPCR-specific
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