Division of Electronics, Ruđer Bošković Institute, Zagreb, Croatia.
Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia.
Sci Rep. 2024 Apr 20;14(1):9062. doi: 10.1038/s41598-024-59312-z.
Head and neck cancer is the sixth most common malignancy worldwide, with the relatively low 5-year survival rate, mainly because it is diagnosed at a late stage. Infection with HPV is a well known aetiology, which affects the nature of these cancers and patients' survival. Besides, it is considered that the main driving force for this type of cancer could be epigenetics. In this study we aimed to find potential epigenetic biomarkers, by integrating miRNome, methylome, and transcriptome analyses. From the fresh head and neck cancer tissue samples, we chose a group for miRNome, methylome and transcriptome profiling, in comparison to adequate control samples. Bioinformatics analyses are performed in R v4.2.2. Count normalisation and group differential expression for mRNA and the previously obtained miRNA count data was performed with DESeq2 v1.36. Gene set enrichment analysis was performed and visualised using gProfiler2 v0.2.1 Identification of miRNA targets was performed by querying in miRTarBase using multiMiR v1.18.0. Annotation of CpG sites merging into islands was obtained from RnBeads.hg19 v1.28.0. package. For the integrative analysis we performed kmeans clustering using stats v4.2.2 package, using 8-12 clusters and nstart 100. We found that transcriptome analysis divides samples into cancers and controls clusters, with no relation to HPV status or cancer anatomical location. Differentially expressed genes (n = 2781) were predominantly associated with signalling pathways of tumour progression. We identified a cluster of genes under the control of the transcription factor E2F that are significantly underexpressed in cancer tissue, as well as T cell immunity genes and genes related to regulation of transcription. Among overexpressed genes in tumours we found those that belong to cell cycle regulation and vasculature. A small number of genes were found significantly differentially expressed in HPV-positive versus HPV-negative tumours (for example NEFH, ZFR2, TAF7L, ZNF541, and TYMS). In this comprehensive study on an overlapping set of samples where the integration of miRNome, methylome and transcriptome analysis were performed for head and neck cancer, we demonstrated that the majority of genes were associated exclusively with miRNome or methylome and, to a lesser extent, under the control of both epigenetic mechanisms.
头颈部癌症是全球第六大常见恶性肿瘤，其 5 年生存率相对较低，主要是因为它在晚期才被诊断出来。HPV 感染是一种众所周知的病因，它影响这些癌症的性质和患者的生存率。此外，人们认为这种癌症的主要驱动力可能是表观遗传学。在这项研究中，我们旨在通过整合 miRNA 组、甲基化组和转录组分析来寻找潜在的表观遗传生物标志物。我们从新鲜的头颈部癌组织样本中选择了一组进行 miRNA 组、甲基化组和转录组分析，并与足够的对照样本进行比较。生物信息学分析在 R v4.2.2 中进行。使用 DESeq2 v1.36 对 mRNA 和之前获得的 miRNA 计数数据进行计数归一化和组差异表达分析。使用 gProfiler2 v0.2.1 进行基因集富集分析，并使用 multiMiR v1.18.0 查询 miRTarBase 进行 miRNA 靶标鉴定。CpG 位点与岛融合的注释从 RnBeads.hg19 v1.28.0 包中获得。对于整合分析，我们使用 stats v4.2.2 包进行 kmeans 聚类，使用 8-12 个聚类和 nstart 100。我们发现转录组分析将样本分为癌症和对照聚类，与 HPV 状态或癌症解剖位置无关。差异表达基因(n=2781)主要与肿瘤进展的信号通路相关。我们鉴定了一个受转录因子 E2F 控制的基因簇，这些基因在癌症组织中显著低表达，以及 T 细胞免疫基因和与转录调控相关的基因。在肿瘤中过表达的基因中，我们发现了那些属于细胞周期调节和血管生成的基因。少数基因在 HPV 阳性与 HPV 阴性肿瘤中差异表达显著(例如 NEFH、ZFR2、TAF7L、ZNF541 和 TYMS)。在这项对头颈部癌症进行重叠样本 miRNA 组、甲基化组和转录组分析整合的综合研究中，我们证明了大多数基因仅与 miRNA 组或甲基化组相关，并且在较小程度上受两种表观遗传机制的控制。
