Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer

Lingling Li; Hui Liu; Yan Li; Chunmei Guo; Bing Wang; Dan Shen; Qiao Zhang; Chen Ding

doi:10.1186/s12953-022-00188-0

Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer

Proteome Sci. 2022 Apr 9;20(1):5. doi: 10.1186/s12953-022-00188-0.

Authors

Lingling Li¹, Hui Liu², Yan Li¹, Chunmei Guo¹, Bing Wang², Dan Shen¹, Qiao Zhang¹, Chen Ding^{3

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Affiliations

¹ State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, 200433, China.
² State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China.
³ State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, 200433, China. chend@fudan.edu.cn.
⁴ State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China. chend@fudan.edu.cn.
⁵ Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, China. chend@fudan.edu.cn.

Abstract

Background: 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.

Methods: 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).

Results: 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.

Conclusion: 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.

Keywords: 10,000 phosphosites; Early-stage gastrointestinal cancer; Immune infiltration; Kinases characterization; Proteomics.

Abstract

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