Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling.
Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling.
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DOI：
10.1016/j.isci.2021.102368
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发表时间：
2021-04-23
期刊：
影响因子：
5.8
通讯作者：
Losic B
中科院分区：
文献类型：
--
作者：
Bubie A;Zoulim F;Testoni B;Miles B;Posner M;Villanueva A;Losic B
肿瘤病毒基因型和合并感染驱动肿瘤发生的作用仍不清楚。我们已经开发了一种可扩展的高通量工具，用于灵敏和精确的肿瘤病毒基因型去卷积。使用肿瘤RNA测序数据，我们将其应用于537例病毒感染的肝脏，宫颈和头颈部肿瘤，提供了肿瘤病毒基因表达，病毒抗原免疫原性，患者生存率和肿瘤肿瘤病毒基因型组织的突变谱的第一个全面的综合景观。我们发现HBV和HPV基因型和合并感染是患者生存和免疫激活的重要预测因素。最后，我们证明了HPV基因型与病毒癌基因表达的相关性大于癌症类型，这意味着在附加型和随机整合型感染中，表达可能是相似的。虽然肿瘤病毒感染是肿瘤发生的已知风险因素，但病毒基因型和合并感染显示与疾病进展、患者生存期、突变特征和推定的肿瘤新抗原免疫原性密切相关，促进了与感染的新临床相关性。ViralMine从原位肿瘤数据中解析肿瘤病毒基因型和共感染TCGA CESC、HNSC和LIHC队列的肿瘤病毒基因分型肿瘤适应性、免疫原性和与肿瘤病毒基因型相关的突变特征基因组学;病毒学;癌症
The role of oncoviral genotype and co-infection driving oncogenesis remains unclear. We have developed a scalable, high throughput tool for sensitive and precise oncoviral genotype deconvolution. Using tumor RNA sequencing data, we applied it to 537 virally infected liver, cervical, and head and neck tumors, providing the first comprehensive integrative landscape of tumor-viral gene expression, viral antigen immunogenicity, patient survival, and mutational profiling organized by tumor oncoviral genotype. We find that HBV and HPV genotype and co-infection serve as significant predictors of patient survival and immune activation. Finally, we demonstrate that HPV genotype is more associated with viral oncogene expression than cancer type, implying that expression may be similar across episomal and stochastic integration-based infections. While oncoviral infections are known risk factors for oncogenesis, viral genotype and co-infection are shown to strongly associate with disease progression, patient survival, mutational signatures, and putative tumor neoantigen immunogenicity, facilitating novel clinical associations with infections. ViralMine parses oncoviral genotypes and co-infection from in situ tumor data Oncoviral genotyping of TCGA CESC, HNSC, and LIHC cohorts Tumor fitness, immunogenicity, and mutational signatures associate with oncoviral genotype Genomics; Virology; Cancer
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影响因子：
30.8
作者：
Burns, Michael B.;Temiz, Nuri A.;Harris, Reuben S.
通讯作者：
Harris, Reuben S.
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
DOI：
10.1007/978-1-0716-0327-7_10
发表时间：
2020-01-01
期刊：
BIOINFORMATICS FOR CANCER IMMUNOTHERAPY
影响因子：
--
作者：
Kodysh, Julia;Rubinsteyn, Alex
通讯作者：
Rubinsteyn, Alex
影响因子：
30.8
作者：
Miao D;Margolis CA;Vokes NI;Liu D;Taylor-Weiner A;Wankowicz SM;Adeegbe D;Keliher D;Schilling B;Tracy A;Manos M;Chau NG;Hanna GJ;Polak P;Rodig SJ;Signoretti S;Sholl LM;Engelman JA;Getz G;Jänne PA;Haddad RI;Choueiri TK;Barbie DA;Haq R;Awad MM;Schadendorf D;Hodi FS;Bellmunt J;Wong KK;Hammerman P;Van Allen EM
通讯作者：
Van Allen EM
DOI：
10.1007/978-81-322-2413-6_2
发表时间：
2015-01-01
期刊：
HPV AND HEAD AND NECK CANCERS
影响因子：
--
作者：
Dahlstrom, Kristina R.;Sturgis, Erich M.
通讯作者：
Sturgis, Erich M.