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

Abstract

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.

• Authors: Xin Ku, Qiangling Sun, Lei Zhu, Zhitao Gu, Yuchen Han, Ning Xu, Chen Meng, Xiaohua Yang, Wei Yan, Wentao Fang
• Journal: Molecular oncology (Mol Oncol) Vol. 14 Issue 4 Pg. 721-741 (04 2020) ISSN: 1878-0261 [Electronic] United States
• PMID: 31967407 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © 2020 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

Chemical References

• Biomarkers, Tumor
• CNOT2 protein, human
• CNOT9 protein, human
• Proteome
• Repressor Proteins
• Transcription Factors
• Glycine Hydroxymethyltransferase
• SHMT protein, human

Topics

• Adult
• Aged
• Biomarkers, Tumor (analysis)
• Female
• Glycine Hydroxymethyltransferase (analysis)
• Humans
• Male
• Middle Aged
• Neoplasms, Glandular and Epithelial (diagnosis, pathology)
• Prognosis
• Proteome (analysis)
• Proteomics
• Repressor Proteins (analysis)
• Thymus Neoplasms (diagnosis, pathology)
• Transcription Factors (analysis)