Applied Biosciences, Faculty of Science and Engineering, Macquarie University, Sydney 2109, Australia.
Int J Mol Sci. 2023 Jan 5;24(2):1050. doi: 10.3390/ijms24021050.
Oral squamous cell carcinoma (OSCC) is the most common head and neck malignancy, with an estimated 5-year survival rate of only 40-50%, largely due to late detection and diagnosis. Emerging evidence suggests that the human microbiome may be implicated in OSCC, with oral microbiome studies putatively identifying relevant bacterial species. As the impact of other microbial organisms, such as fungi and viruses, has largely been neglected, a bioinformatic approach utilizing the Trans-Proteomic Pipeline (TPP) and the R statistical programming language was implemented here to investigate not only bacteria, but also viruses and fungi in the context of a publicly available, OSCC, mass spectrometry (MS) dataset. Overall viral, bacterial, and fungal composition was inferred in control and OSCC patient tissue from protein data, with a range of proteins observed to be differentially enriched between healthy and OSCC conditions, of which the fungal protein profile presented as the best potential discriminator of OSCC within the analysed dataset. While the current project sheds new light on the fungal and viral spheres of the oral microbiome in cancer in silico, further research will be required to validate these findings in an experimental setting.
口腔鳞状细胞癌（OSCC）是最常见的头颈部恶性肿瘤，5 年生存率估计仅为 40-50%，主要原因是晚期发现和诊断。新出现的证据表明，人类微生物组可能与 OSCC 有关，口腔微生物组研究推测出相关的细菌种类。由于其他微生物（如真菌和病毒）的影响在很大程度上被忽视，因此这里采用了一种利用跨蛋白质组学管道（TPP）和 R 统计编程语言的生物信息学方法，不仅研究了细菌，还研究了病毒和真菌在公开的 OSCC 质谱（MS）数据集的背景下。从蛋白质数据中推断出对照组和 OSCC 患者组织中的整体病毒、细菌和真菌组成，观察到许多蛋白质在健康和 OSCC 条件之间存在差异富集，其中真菌蛋白谱在分析的数据集内呈现出 OSCC 的最佳潜在区分者。虽然当前的项目在计算机上为癌症的口腔微生物组的真菌和病毒领域提供了新的认识，但需要进一步的研究来在实验环境中验证这些发现。
