Loss of cell differentiation is a hallmark for the progression of oral squamous cell carcinoma (OSCC). Archival Formalin-Fixed Paraffin-Embedded (FFPE) tissues constitute a valuable resource for studying the differentiation of OSCC and can offer valuable insights into the process of tumor progression. In the current study, we performed LC–MS/MS-based quantitative proteomics of FFPE specimens from pathologically-confirmed well-differentiated, moderately-differentiated, and poorly-differentiated OSCC cases. The data were analyzed in four technical replicates, resulting in the identification of 2376 proteins. Of these, 141 and 109 were differentially expressed in moderately-differentiated and poorly differentiated OSCC cases, respectively, compared to well-differentiated OSCC. The data revealed significant metabolic reprogramming with respect to lipid metabolism and glycolysis with proteins belonging to both these processes downregulated in moderately-differentiated OSCC when compared to well-differentiated OSCC. Signaling pathway analysis indicated the alteration of extracellular matrix organization, muscle contraction, and glucose metabolism pathways across tumor grades. The extracellular matrix organization pathway was upregulated in moderately-differentiated OSCC and downregulated in poorly differentiated OSCC, compared to well-differentiated OSCC. PADI4, an epigenetic enzyme transcriptional regulator, and its transcriptional target HIST1H1B were both found to be upregulated in moderately differentiated and poorly differentiated OSCC, indicating epigenetic events underlying tumor differentiation. In conclusion, the findings support the advantage of using high-resolution mass spectrometry-based FFPE archival blocks for clinical and translational research. The candidate signaling pathways identified in the study could be used to develop potential therapeutic targets for OSCC.

细胞分化的丧失是口腔鳞状细胞癌 (OSCC) 进展的标志。存档的福尔马林固定石蜡包埋 (FFPE) 组织是研究 OSCC 分化的宝贵资源，可以为肿瘤进展过程提供有价值的见解。在目前的研究中，我们对来自病理证实的高分化、中分化和低分化 OSCC 病例的 FFPE 标本进行了基于 LC-MS/MS 的定量蛋白质组学。对数据进行了四次技术重复分析，最终鉴定出 2376 种蛋白质。其中，与分化良好的 OSCC 相比，141 个和 109 个分别在中分化和低分化 OSCC 病例中差异表达。数据显示，与分化良好的 OSCC 相比，中度分化的 OSCC 中属于这两个过程的蛋白质在脂质代谢和糖酵解方面发生了显着的代谢重编程。信号通路分析表明跨肿瘤级别的细胞外基质组织、肌肉收缩和葡萄糖代谢通路的改变。与分化良好的 OSCC 相比，细胞外基质组织途径在中度分化的 OSCC 中上调，在低分化的 OSCC 中下调。PADI4（一种表观遗传酶转录调节因子）及其转录靶标 HIST1H1B 在中分化和低分化 OSCC 中均被上调，表明肿瘤分化的表观遗传事件。综上所述，研究结果支持使用基于高分辨率质谱的 FFPE 档案块进行临床和转化研究的优势。该研究中确定的候选信号通路可用于开发 OSCC 的潜在治疗靶点。