Viollet Coralie, Davis David A, Reczko Martin, Ziegelbauer Joseph M, Pezzella Francesco, Ragoussis Jiannis, Yarchoan Robert
HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America; The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
PLoS One. 2015 May 5;10(5):e0126439. doi: 10.1371/journal.pone.0126439. eCollection 2015.
Kaposi's sarcoma associated herpesvirus (KSHV) causes several tumors, including primary effusion lymphoma (PEL) and Kaposi's sarcoma (KS). Cellular and viral microRNAs (miRNAs) have been shown to play important roles in regulating gene expression. A better knowledge of the miRNA-mediated pathways affected by KSHV infection is therefore important for understanding viral infection and tumor pathogenesis. In this study, we used deep sequencing to analyze miRNA and cellular mRNA expression in a cell line with latent KSHV infection (SLKK) as compared to the uninfected SLK line. This approach revealed 153 differentially expressed human miRNAs, eight of which were independently confirmed by qRT-PCR. KSHV infection led to the dysregulation of ~15% of the human miRNA pool and most of these cellular miRNAs were down-regulated, including nearly all members of the 14q32 miRNA cluster, a genomic locus linked to cancer and that is deleted in a number of PEL cell lines. Furthermore, we identified 48 miRNAs that were associated with a total of 1,117 predicted or experimentally validated target mRNAs; of these mRNAs, a majority (73%) were inversely correlated to expression changes of their respective miRNAs, suggesting miRNA-mediated silencing mechanisms were involved in a number of these alterations. Several dysregulated miRNA-mRNA pairs may facilitate KSHV infection or tumor formation, such as up-regulated miR-708-5p, associated with a decrease in pro-apoptotic caspase-2 and leukemia inhibitory factor LIF, or down-regulated miR-409-5p, associated with an increase in the p53-inhibitor MDM2. Transfection of miRNA mimics provided further evidence that changes in miRNAs are driving some observed mRNA changes. Using filtered datasets, we also identified several canonical pathways that were significantly enriched in differentially expressed miRNA-mRNA pairs, such as the epithelial-to-mesenchymal transition and the interleukin-8 signaling pathways. Overall, our data provide a more detailed understanding of KSHV latency and guide further studies of the biological significance of these changes.
卡波西肉瘤相关疱疹病毒（KSHV）可引发多种肿瘤，包括原发性渗出性淋巴瘤（PEL）和卡波西肉瘤（KS）。细胞和病毒微小RNA（miRNA）已被证明在调节基因表达中发挥重要作用。因此，更好地了解受KSHV感染影响的miRNA介导的途径对于理解病毒感染和肿瘤发病机制至关重要。在本研究中，我们使用深度测序分析了潜伏性KSHV感染的细胞系（SLKK）与未感染的SLK细胞系中miRNA和细胞mRNA的表达。该方法揭示了153种差异表达的人类miRNA，其中8种通过qRT-PCR独立验证。KSHV感染导致约15%的人类miRNA库失调，这些细胞miRNA大多下调，包括14q32 miRNA簇的几乎所有成员，该基因组位点与癌症相关且在许多PEL细胞系中缺失。此外，我们鉴定出48种miRNA，它们与总共1117种预测或实验验证的靶标mRNA相关；在这些mRNA中，大多数（73%）与其各自miRNA的表达变化呈负相关，表明miRNA介导的沉默机制参与了其中许多改变。几个失调的miRNA-mRNA对可能促进KSHV感染或肿瘤形成，例如上调的miR-708-5p与促凋亡半胱天冬酶-2和白血病抑制因子LIF的减少相关，或下调的miR-409-5p与p53抑制剂MDM2的增加相关。转染miRNA模拟物提供了进一步的证据，表明miRNA的变化驱动了一些观察到的mRNA变化。使用过滤后的数据集，我们还确定了在差异表达的miRNA-mRNA对中显著富集的几个经典途径，如上皮-间质转化和白细胞介素-8信号通路。总体而言，我们的数据提供了对KSHV潜伏期更详细的理解，并指导对这些变化的生物学意义的进一步研究。
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