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

Ku, Xin; Sun, Qiangling; Zhu, Lei; Gu, Zhitao; Han, Yuchen; Xu, Ning; Meng, Chen; Yang, Xiaohua; Yan, Wei; Fang, Wentao

doi:10.1002/1878-0261.12642

Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS)

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Title:: Deciphering tissue‐based proteome signatures revealed novel subtyping and prognostic markers for thymic epithelial tumors
Document type:: Zeitschriftenaufsatz
Author(s):: Ku, Xin; Sun, Qiangling; Zhu, Lei; Gu, Zhitao; Han, Yuchen; Xu, Ning; Meng, Chen; Yang, Xiaohua; Yan, Wei; Fang, Wentao
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 managment. © 2020 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.
Keywords:: BayBioMS; Molecular Profiling; Protein classifiers; Targeted Proteomics; Thymic epithelial tumors; WHO classification
Journal title:: Molecular Oncology
Year:: 2020
Fulltext / DOI:: doi:10.1002/1878-0261.12642
Publisher:: Wiley
E-ISSN:: 1574-78911878-0261
Date of publication:: 22.01.2020
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mediaTUM Gesamtbestand Einrichtungen Schools TUM School of Life Sciences Zentren Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS)Jahr 2020

mediaTUM Gesamtbestand Hochschulbibliographie 2020 Fakultäten Wissenschaftszentrum Weihenstephan Bayerisches Zentrum für Biomolekulare Massenspektrometrie (BayBioMS)