Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes

We have developed a novel computational approach for detecting viral transcripts in human cancers applicable to a wide variety of viruses and tumors that takes the aforementioned confounding factors into account. We apply the approach to conducting the first systematic search for viruses in neuroblastoma, the most common cancer in infancy. The diverse clinical progression of this disease as well as related epidemiological and virological findings are highly suggestive of a pathogenic cofactor. However, a viral etiology of neuroblastoma is currently contested. We mapped 14 transcriptomes of neuroblastoma as well as several positive control transcriptomes to the human and all known viral genomes in order to detect both known and unknown viruses. Analysis of positive controls, comparisons with related methods, and statistical estimates demonstrate the high sensitivity of our approach. However, detailed analysis of putative vi- ral transcripts within neuroblastoma samples did not provide evidence for the existence of any known human viruses. Likewise, de-novo assembly and analysis of chimeric transcripts did not result in expression signatures associated with novel human pathogens. While confounding factors such as sample dilution or viral clearance in progressed tumors may mask viral cofactors in the data, in principle, this is rendered less likely by the high sensitivity of our approach and the number of biological replicates analyzed. Therefore, our results suggest that frequent viral cofactors of metastatic neuroblastoma are unlikely.

本研究开发了一种新型计算方法，用于检测人类癌症中的病毒转录本（viral transcripts），该方法可适配多种病毒与肿瘤类型，并纳入了前述混杂因素的考量。我们将该方法应用于首个针对神经母细胞瘤（neuroblastoma）——婴儿期最常见的恶性肿瘤——的系统性病毒筛查研究。该疾病存在多样化的临床进展特征，结合相关流行病学及病毒学研究结果，强烈提示存在致病性辅因子。但目前学界对于神经母细胞瘤的病毒病因假说仍存在争议。我们将14份神经母细胞瘤转录组（transcriptomes）及多份阳性对照转录组比对至人类基因组与所有已知病毒基因组，以实现已知与未知病毒的检测。对阳性对照的分析、与同类方法的对比以及统计学评估均证实，本方法具有极高的检测灵敏度。然而，对神经母细胞瘤样本中疑似病毒转录本的详细分析并未发现任何已知人类病毒存在的证据。同样，对嵌合转录本（chimeric transcripts）的从头组装与分析也未得到与新型人类病原体相关的表达特征。尽管样本稀释、进展期肿瘤中的病毒清除等混杂因素可能掩盖数据中的病毒辅因子信号，但从原理上讲，本方法的高灵敏度以及所分析的生物学重复样本数量，使得这种情况发生的可能性大幅降低。因此，本研究结果提示，转移性神经母细胞瘤频繁携带病毒辅因子的可能性极低。