Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.
Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Front Immunol. 2023 Jan 13;13:1096494. doi: 10.3389/fimmu.2022.1096494. eCollection 2022.
Testicular germ cell tumor (TGCT) is the most common tumor in young men, but molecular signatures, especially the alternative splicing (AS) between its subtypes have not yet been explored.
To investigate the differences between TGCT subtypes, we comprehensively analyzed the data of gene expression, alternative splicing (AS), and somatic mutation in TGCT patients from the TCGA database. The gene ontology (GO) enrichment analyses were used to explore the function of differentially expressed genes and spliced genes respectively, and Spearman correlation analysis was performed to explore the correlation between differential genes and AS events. In addition, the possible patterns in which AS regulates gene expression were elaborated by the ensemble database transcript atlas. And, we identified important transcription factors that regulate gene expression and AS and functionally validated them in TGCT cell lines.
We found significant differences between expression and AS in embryonal carcinoma and seminoma, while mixed cell tumors were in between. GO enrichment analyses revealed that both differentially expressed and spliced genes were enriched in transcriptional regulatory pathways, and obvious correlation between expression and AS events was determined. By analyzing the transcript map and the sites where splicing occurs, we have demonstrated that AS regulates gene expression in a variety of ways. We further identified two pivot AS-related molecules (SOX2 and HDAC9) involved in AS regulation, which were validated in embryonal carcinoma and seminoma cell lines. Differences in somatic mutations between subtypes are also of concern, with our results suggesting that mutations in some genes (B3GNT8, CAPN7, FAT4, GRK1, TACC2, and TRAM1L1) occur only in embryonal carcinoma, while mutations in KIT, KARS, and NRAS are observed only in seminoma.
In conclusion, our analysis revealed the differences in gene expression, AS and somatic mutation among TGCT subtypes, providing a molecular basis for clinical diagnosis and precise therapy of TGCT patients.
睾丸生殖细胞肿瘤（TGCT）是年轻男性中最常见的肿瘤，但分子特征，尤其是其亚型之间的选择性剪接（AS）尚未得到探索。
为了研究 TGCT 亚型之间的差异，我们综合分析了 TCGA 数据库中 TGCT 患者的基因表达、选择性剪接（AS）和体细胞突变数据。通过基因本体论（GO）富集分析分别探索差异表达基因和剪接基因的功能，并进行 Spearman 相关性分析，以探索差异基因与 AS 事件之间的相关性。此外，通过集成数据库转录图谱阐述了 AS 调节基因表达的可能模式。并鉴定了调节基因表达和 AS 的重要转录因子，并在 TGCT 细胞系中对其进行了功能验证。
我们发现胚胎癌和精原细胞瘤之间在表达和 AS 上存在显著差异，而混合细胞瘤则介于两者之间。GO 富集分析表明，差异表达和剪接基因均富集在转录调控途径中，并且确定了表达和 AS 事件之间的明显相关性。通过分析转录图谱和剪接发生的位点，我们已经证明 AS 以多种方式调节基因表达。我们进一步确定了两个涉及 AS 调节的枢纽 AS 相关分子（SOX2 和 HDAC9），并在胚胎癌和精原细胞瘤细胞系中进行了验证。亚型之间的体细胞突变差异也值得关注，我们的结果表明，某些基因（B3GNT8、CAPN7、FAT4、GRK1、TACC2 和 TRAM1L1）中的突变仅发生在胚胎癌中，而 KIT、KARS 和 NRAS 中的突变仅发生在精原细胞瘤中。
总之，我们的分析揭示了 TGCT 亚型之间基因表达、AS 和体细胞突变的差异，为 TGCT 患者的临床诊断和精准治疗提供了分子基础。
