Deciphering tissue‐based proteome signatures revealed novel subtyping and prognostic markers for thymic epithelial tumors

• Published in: Molecular oncology Vol. 14; no. 4; pp. 721 - 741
• Main Authors: Ku, Xin, Sun, Qiangling, Zhu, Lei, Gu, Zhitao, Han, Yuchen, Xu, Ning, Meng, Chen, Yang, Xiaohua, Yan, Wei, Fang, Wentao
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.04.2020; John Wiley and Sons Inc; Wiley
• Subjects: Adult; Aged; Biomarkers, Tumor - analysis; Female; Glycine; Glycine Hydroxymethyltransferase - analysis; Homogenization; Humans; Lymphocytes; Male; Mass spectroscopy; Middle Aged; molecular profiling; mRNA; Neoplasms, Glandular and Epithelial - diagnosis; Neoplasms, Glandular and Epithelial - pathology; Patients; Peptides; Principal components analysis; Prognosis; protein classifiers; Proteins; Proteome - analysis; Proteomes; Proteomics; Repressor Proteins - analysis; Serine; Squamous cell carcinoma; Studies; targeted proteomics; thymic epithelial tumors; Thymus; Thymus Neoplasms - diagnosis; Thymus Neoplasms - pathology; Transcription Factors - analysis; Tumors; WHO classification; protein classifiers; thymic epithelial tumors; targeted proteomics; WHO classification; molecular profiling
• ISSN: 1574-7891; 1878-0261
• DOI: 10.1002/1878-0261.12642

Thymic epithelial tumors (TETs) belong to a group of tumors that rarely occur, but have unresolved mechanisms and heterogeneous clinical behaviors. Current care of TET patients demands biomarkers of high sensitivity and specificity for accurate histological classification and prognosis management. In this study, 134 fresh‐frozen tissue samples (84 tumor, 40 tumor adjacent, and 10 normal thymus) were recruited to generate a quantitative and systematic view of proteomic landscape of TETs. Among them, 90 samples were analyzed by data‐independent acquisition mass spectrometry (DIA‐MS) leading to discovery of novel classifying molecules among different TET subtypes. The correlation between clinical outcome and the identified molecules was probed, and the prioritized proteins of interest were further validated on the remaining samples (n = 44) via parallel reaction monitoring (PRM) as well as immunohistochemical and confocal imaging analysis. In particular, two proteins, the cellular mRNA deadenylase CCR4 (carbon catabolite repressor 4)‐NOT (negative on TATA) complex subunit 2/9 (CNOT2/9) and the serine hydroxymethyltransferase that catalyzes the reversible interconversions of serine and glycine (SHMT1), were found at dramatic low levels in the thymic epithelia of more malignant subtype, thymic squamous cell carcinoma (TSCC). Interestingly, the mRNA levels of these two genes were shown to be closely correlated with prognosis of the TET patients. These results extended the existing human tissue proteome atlas and allowed us to identify several new protein classifiers for TET subtyping. Newly identified subtyping and prognosis markers, CNOT2/9 and SHMT1, will expand current diagnostic arsenal in terms of higher specificity and prognostic insights for TET diagnosis and management. Thymic epithelial tumors (TETs) belong to a group of tumors that rarely occur, but have unresolved mechanisms and heterogeneous clinical behaviors. Current care of TET patients demands protein biomarkers of high sensitivity and specificity for accurate histological classification. In this study, we surveyed 134 tissue proteomes, identified, and validated a suite of protein classifiers associated with different TET subtypes.