Department of Pathology, Tulane University, New Orleans, LA, 70112, USA.
Tulane Cancer Center, New Orleans, LA, 70112, USA.
Acta Neuropathol Commun. 2016 Jul 11;4(1):71. doi: 10.1186/s40478-016-0338-z.
Next generation sequencing (NGS) can globally interrogate the genetic composition of biological samples in an unbiased yet sensitive manner. The objective of this study was to utilize the capabilities of NGS to investigate the reported association between glioblastoma multiforme (GBM) and human cytomegalovirus (HCMV). A large-scale comprehensive virome assessment was performed on publicly available sequencing datasets from the Cancer Genome Atlas (TCGA), including RNA-seq datasets from primary GBM (n = 157), recurrent GBM (n = 13), low-grade gliomas (n = 514), recurrent low-grade gliomas (n = 17), and normal brain (n = 5), and whole genome sequencing (WGS) datasets from primary GBM (n = 51), recurrent GBM (n = 10), and normal matched blood samples (n = 20). In addition, RNA-seq datasets from MRI-guided biopsies (n = 92) and glioma stem-like cell cultures (n = 9) were analyzed. Sixty-four DNA-seq datasets from 11 meningiomas and their corresponding blood control samples were also analyzed. Finally, three primary GBM tissue samples were obtained, sequenced using RNA-seq, and analyzed. After in-depth analysis, the most robust virus findings were the detection of papillomavirus (HPV) and hepatitis B reads in the occasional LGG sample (4 samples and 1 sample, respectively). In addition, low numbers of virus reads were detected in several datasets but detailed investigation of these reads suggest that these findings likely represent artifacts or non-pathological infections. For example, all of the sporadic low level HCMV reads were found to map to the immediate early promoter intimating that they likely originated from laboratory expression vector contamination. Despite the detection of low numbers of Epstein-Barr virus reads in some samples, these likely originated from infiltrating B-cells. Finally, human herpesvirus 6 and 7 aligned viral reads were identified in all DNA-seq and a few RNA-seq datasets but detailed analysis demonstrated that these were likely derived from the homologous human telomeric-like repeats. Other low abundance viral reads were detected in some samples but for most viruses, the reads likely represent artifacts or incidental infections. This analysis argues against associations between most known viruses and GBM or mengiomas. Nevertheless, there may be a low percentage association between HPV and/or hepatitis B and LGGs.
下一代测序 (NGS) 可以无偏倚但敏感地全局检测生物样本的遗传组成。本研究的目的是利用 NGS 的能力来研究胶质母细胞瘤多形性 (GBM) 与人类巨细胞病毒 (HCMV) 之间的报告关联。对癌症基因组图谱 (TCGA) 中公开可用的测序数据集进行了大规模综合病毒组评估，包括来自原发性 GBM（n=157）、复发性 GBM（n=13）、低级别胶质瘤（n=514）、复发性低级别胶质瘤（n=17）和正常脑（n=5）的 RNA-seq 数据集，以及来自原发性 GBM（n=51）、复发性 GBM（n=10）和正常匹配血液样本（n=20）的全基因组测序 (WGS) 数据集。此外，还分析了 MRI 引导活检（n=92）和神经胶质瘤干细胞培养物（n=9）的 RNA-seq 数据集。还分析了来自 11 例脑膜瘤及其相应血液对照样本的 64 个 DNA-seq 数据集。最后，获得了 3 例原发性 GBM 组织样本，使用 RNA-seq 进行测序并进行分析。经过深入分析，最可靠的病毒发现是在偶尔的 LGG 样本中检测到乳头瘤病毒 (HPV) 和乙型肝炎病毒读段（分别为 4 个样本和 1 个样本）。此外，在几个数据集检测到少量病毒读段，但对这些读段的详细调查表明，这些发现可能代表人工制品或非病理性感染。例如，所有散发性低水平 HCMV 读段都被发现映射到早期启动子，暗示它们可能源自实验室表达载体污染。尽管在一些样本中检测到少量 EBV 读段，但这些可能源自浸润 B 细胞。最后，在所有 DNA-seq 和一些 RNA-seq 数据集中都鉴定出人类疱疹病毒 6 和 7 对齐的病毒读段，但详细分析表明这些可能源自同源人端粒样重复。在一些样本中检测到其他低丰度病毒读段，但对于大多数病毒，这些读段可能代表人工制品或偶然感染。该分析反对大多数已知病毒与 GBM 或脑膜瘤之间的关联。然而，HPV 和/或乙型肝炎病毒与 LGG 之间可能存在低百分比的关联。
