The surveillance and therapy of early-stage cancer would be better for patients’ prognosis. However, the extreme trace amount of tissue samples in different stages have limited in portraying the characterization of early-stage cancer. Therefore, we focused on and presented comprehensive proteomic and phosphoproproteomic profiling of the trace FFPE samples from early-stage gastrointestinal cancer, and then explored the potential biomarkers of early-stage gastrointestinal cancer. In this study, a quantitative proteomic method with chromatography with mass spectrometry (LC-MS/MS) was used to analyse the proteomic difference between the trace early-stage esophageal squamous cell carcinoma (EESCC) and early-stage duodenum adenocarcinoma cancer (EDAC). We identified ~ 6000 proteins and > 10,000 phosphosites in single trace FFPE samples. Comparative analysis disclosed the diverse proteomic features of tumor tissues compared with paired normal tissue of EESCC and EDAC, and revealed the difference of EESCC and EDAC was derived from their origin normal tissue. The distinct separation of EESCC and EDAC illustrated the functions of cell cycle (RB1 T373, EGFR T693) in EESCC, and the positive impacts of apoptosis, metabolic processes (MTOR and MTOR S1261) in EDAC. Furthermore, we deconvoluted the immune infiltration of early-stage gastrointestinal cancer, in which higher immune cell signatures were detected in EDAC, and showed the specific cytokines in EESCC and EDAC. We performed kinases-substates relationship analysis and elucidated the specific proteomic kinase characterization of EESCC and EDAC, and proposed the medicative effects and corresponding drugs for EESCC and EDAC at the clinic. We disclosed the specific immune characterization of the early-stage gastrointestinal cancer, and presented potential makers of EESCC (EGFR, PDGFRB, CDK4, WEE1) and EDAC (MTOR, MAP2K1, MAPK3). This study represents a major stepping stone towards investigating the carcinogenesis mechanism of gastrointestinal cancer, and providing a rich resource for medicative strategy in the clinic.

中文翻译：

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早期胃肠癌中痕量 FFPE 样本的综合蛋白质组学特征

早期癌症的监测和治疗将有利于患者的预后。然而，不同阶段的极微量组织样本在描绘早期癌症的特征方面受到限制。因此，我们专注于并提出了对来自早期胃肠道癌的痕量 FFPE 样本的全面蛋白质组学和磷酸化蛋白质组学分析，然后探索早期胃肠道癌的潜在生物标志物。本研究采用色谱-质谱定量蛋白质组学方法 (LC-MS/MS) 分析微量早期食管鳞状细胞癌 (EESCC) 和早期十二指肠腺癌 (EDAC) 的蛋白质组学差异。 . 我们在单痕量 FFPE 样品中鉴定出约 6000 种蛋白质和 > 10,000 个磷酸位点。对比分析揭示了肿瘤组织与 EESCC 和 EDAC 配对的正常组织相比具有不同的蛋白质组学特征，并揭示 EESCC 和 EDAC 的差异来源于它们的起源正常组织。EESCC 和 EDAC 的明显分离说明了 EESCC 中细胞周期（RB1 T373、EGFR T693）的功能，以及 EDAC 中细胞凋亡、代谢过程（MTOR 和 MTOR S1261）的积极影响。此外，我们对早期胃肠道癌的免疫浸润进行了反卷积，其中在 EDAC 中检测到更高的免疫细胞特征，并在 EESCC 和 EDAC 中显示了特定的细胞因子。我们进行了激酶-亚状态关系分析，并阐明了 EESCC 和 EDAC 的特定蛋白质组激酶表征，并在临床上提出了EESCC和EDAC的药效及相应药物。我们披露了早期胃肠癌的特异性免疫特征，并介绍了 EESCC（EGFR、PDGFRB、CDK4、WEE1）和 EDAC（MTOR、MAP2K1、MAPK3）的潜在制造商。本研究为探索胃肠道癌的致癌机制奠定了重要的基础，为临床用药策略提供了丰富的资源。