Identification of novel prognostic biomarkers for thyroid cancer by integrated transcriptome analysis of metastasis-associated genes

Distant metastasis (DM) is the most important prognostic factor affecting overall survival (OS) of thyroid cancer. The current study aimed to discover prognostic biomarkers to predict thyroid cancer survival, particularly PTC, the most common subtype of thyroid cancer. Four RNA-seq datasets of experimental lung metastasis from 4 transgenic mouse models of PTC, follicular thyroid cancer (FTC), poorly-differentiated thyroid cancer (PDTC), and anaplastic thyroid cancer (ATC) were integrated to screen for candidate genes involved in DM. TCGA-THCA dataset were used to validate the candidate genes. A total of 105 up-regulated and 25 down-regulated differentially expressed genes (DEGs) were identified to be present in all 4 datasets. Regulation of cytokine production, inflammation, immune checkpoint regulation, MAPK/ERK cascade were major enriched pathways in metastatic tumor cells. We identified 7 genes whose overexpression was present in 63 of 498 PTC samples (13%) and was associated with poor OS (p<0.01). Clinically, the 7–gene expression signature was associated with older age at the diagnosis, late stage of tumor, tall-cell variant, and higher aneuploidy and hypoxia score. Mutation load was increased in samples with 7–gene expression signature: 26 samples had more than one driver mutations (47%, 26/55). Deep deletions in other chromosomal locus were frequently found in samples with BRAFV600E point mutations. In contrast, only 7% samples without the 7-gene expression signature had more than one driver mutations (24/243). Increased copy number variants (CNVs) were also observed in metastatic as compared to primary tumor cells such as large deletions and duplications. We conclude that the 7–gene expression signature is associated with poor prognosis and chromosomal instability. It may be a useful biomarker for risk stratification for DM and help decision-making in initial surgical recommendations. Comparative gene expression profiling analysis of RNA-seq datasets between primary and metastatic mouse thyroid cancer cell lines.

远处转移（Distant metastasis, DM）是影响甲状腺癌总生存期（overall survival, OS）的最重要预后因素。本研究旨在发掘可预测甲状腺癌患者生存的预后生物标志物，尤其聚焦于临床最为常见的甲状腺癌亚型——乳头状甲状腺癌（papillary thyroid cancer, PTC）。本研究整合了源自4种转基因小鼠模型的实验性肺转移RNA测序（RNA-seq）数据集，这4种模型分别对应乳头状甲状腺癌、滤泡状甲状腺癌（follicular thyroid cancer, FTC）、低分化甲状腺癌（poorly-differentiated thyroid cancer, PDTC）与未分化甲状腺癌（anaplastic thyroid cancer, ATC），以此筛选参与远处转移的候选基因。后续采用癌症基因组图谱甲状腺癌队列（The Cancer Genome Atlas-Thyroid Carcinoma, TCGA-THCA）数据集对候选基因进行验证。最终在全部4个数据集中共鉴定出105个上调差异表达基因（differentially expressed genes, DEGs）与25个下调差异表达基因。转移瘤细胞中显著富集的核心通路包括细胞因子产生调控、炎症反应、免疫检查点调控以及丝裂原活化蛋白激酶/细胞外调节蛋白激酶（MAPK/ERK）级联反应等。本研究鉴定出7个基因，在498例PTC样本中，有63例（13%）呈现该7个基因的过表达状态，且该过表达与不良总生存期显著相关（p<0.01）。临床分析显示，该7基因表达特征与患者诊断时年龄偏大、肿瘤分期偏晚、高细胞亚型以及非整倍体评分和缺氧评分升高显著相关。携带该7基因表达特征的样本突变负荷更高：55例此类样本中有26例存在至少1个驱动基因突变（占比47%，26/55）。在携带BRAFV600E点突变的样本中，其他染色体位点常出现大片段缺失。与之形成鲜明对比的是，未携带该7基因表达特征的样本中仅有7%存在至少1个驱动基因突变（24/243）。与原发肿瘤细胞相比，转移瘤细胞中也观察到更多拷贝数变异（copy number variants, CNVs），包括大片段缺失与重复。本研究表明，该7基因表达特征与不良预后及染色体不稳定性显著相关，可作为远处转移风险分层的有效生物标志物，辅助临床制定初始手术治疗方案的决策。本研究还针对小鼠甲状腺癌原发与转移细胞系的RNA测序数据集开展了比较基因表达谱分析。