Chicard Mathieu, Iddir Yasmine, Masliah Planchon Julien, Combaret Valérie, Attignon Valéry, Saint-Charles Alexandra, Frappaz Didier, Faure-Conter Cécile, Beccaria Kévin, Varlet Pascale, Geoerger Birgit, Baulande Sylvain, Pierron Gaelle, Bouchoucha Yassine, Doz François, Delattre Olivier, Waterfall Joshua J, Bourdeaut Franck, Schleiermacher Gudrun
Recherche Translationelle en Oncologie Pédiatrique (RTOP), INSERM U830 Cancer, Heterogeneity, Instability and Plasticity, Department of Translational Research, Institut Curie Research Center, PSL Research University, 75005 Paris, France.
Unité de Génétique Somatique, Service de Génétique, Institut Curie Hospital Group, 75005 Paris, France.
Cancers (Basel). 2023 Jul 7;15(13):3532. doi: 10.3390/cancers15133532.
Liquid biopsies are revolutionary tools used to detect tumor-specific genetic alterations in body fluids, including the use of cell-free DNA (cfDNA) for molecular diagnosis in cancer patients. In brain tumors, cerebrospinal fluid (CSF) cfDNA might be more informative than plasma cfDNA. Here, we assess the use of CSF cfDNA in pediatric embryonal brain tumors (EBT) for molecular diagnosis.
The CSF cfDNA of pediatric patients with medulloblastoma ( = 18), ATRT ( = 3), ETMR ( = 1), CNS NB FOXR2 ( = 2) and pediatric EBT NOS ( = 1) (mean cfDNA concentration 48 ng/mL; range 4-442 ng/mL) and matched tumor genomic DNA were sequenced by WES and/or a targeted sequencing approach to determine single-nucleotide variations (SNVs) and copy number alterations (CNA). A specific capture covering transcription start sites (TSS) of genes of interest was also used for nucleosome footprinting in CSF cfDNA.
15/25 CSF cfDNA samples yielded informative results, with informative CNA and SNVs in 11 and 15 cases, respectively. For cases with paired tumor and CSF cfDNA WES ( = 15), a mean of 83 (range 1-160) shared SNVs were observed, including SNVs in classical medulloblastoma genes such as SMO and KMT2D. Interestingly, tumor-specific SNVs (mean 18; range 1-62) or CSF-specific SNVs (mean 5; range 0-25) were also observed, suggesting clonal heterogeneity. The TSS panel resulted in differential coverage profiles across all 112 studied genes in 7 cases, indicating distinct promoter accessibility.
CSF cfDNA sequencing yielded informative results in 60% (15/25) of all cases, with informative results in 83% (15/18) of all cases analyzed by WES. These results pave the way for the implementation of these novel approaches for molecular diagnosis and minimal residual disease monitoring.
液体活检是用于检测体液中肿瘤特异性基因改变的革命性工具，包括使用游离DNA（cfDNA）对癌症患者进行分子诊断。在脑肿瘤中，脑脊液（CSF）cfDNA可能比血浆cfDNA提供更多信息。在此，我们评估CSF cfDNA在儿童胚胎性脑肿瘤（EBT）分子诊断中的应用。
对患有髓母细胞瘤（n = 18）、非典型畸胎样/横纹肌样肿瘤（ATRT，n = 3）、胚胎性肿瘤伴有多层玫瑰花结（ETMR，n = 1）、中枢神经系统神经母细胞瘤FOXR2改变（CNS NB FOXR2，n = 2）和儿童EBT未特指（EBT NOS，n = 1）的儿科患者的CSF cfDNA（平均cfDNA浓度48 ng/mL；范围4 - 442 ng/mL）以及匹配的肿瘤基因组DNA进行全外显子测序（WES）和/或靶向测序，以确定单核苷酸变异（SNV）和拷贝数改变（CNA）。还使用了覆盖感兴趣基因转录起始位点（TSS）的特异性捕获方法对CSF cfDNA进行核小体足迹分析。
25份CSF cfDNA样本中有15份产生了有用结果，分别在11例和15例中发现了有用的CNA和SNV。对于肿瘤和CSF cfDNA进行配对WES的病例（n = 15），平均观察到83个（范围1 - ）共享SNV，包括经典髓母细胞瘤基因如SMO和KMT2D中的SNV。有趣的是，还观察到肿瘤特异性SNV（平均18个；范围1 - 62）或CSF特异性SNV（平均5个；范围0 - 25），提示克隆异质性。TSS分析在7例中对所有112个研究基因产生了不同的覆盖图谱，表明启动子可及性不同。
CSF cfDNA测序在所有病例的60%（15/25）中产生了有用结果，在通过WES分析的所有病例的83%（15/18）中产生了有用结果。这些结果为实施这些用于分子诊断和微小残留病监测的新方法铺平了道路。 （原文中“range 1 - ”处似乎有信息缺失，已按原文翻译）
