Identification of TUBB2A by quantitative proteomic analysis as a novel biomarker for the prediction of distant metastatic breast cancer

Dongyoon Shin; Joonho Park; Dohyun Han; Ji Hye Moon; Han Suk Ryu; Youngsoo Kim

doi:10.1186/s12014-020-09280-z

Identification of TUBB2A by quantitative proteomic analysis as a novel biomarker for the prediction of distant metastatic breast cancer

Clin Proteomics. 2020 May 24:17:16. doi: 10.1186/s12014-020-09280-z. eCollection 2020.

Authors

Dongyoon Shin^#¹, Joonho Park^#², Dohyun Han³, Ji Hye Moon⁴, Han Suk Ryu⁴, Youngsoo Kim^{1

2}

Affiliations

¹ Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehakro, Seoul, 30380 Korea.
² Interdisciplinary Program for Bioengineering, Seoul National University College of Engineering, Seoul, Korea.
³ Biomedical Research Institute, Seoul National University Hospital, 101 Daehakro, Seoul, Korea.
⁴ Department of Pathology, Seoul National University Hospital, 101 Daehakro, Seoul, 03080 Korea.

^# Contributed equally.

Abstract

Background: Metastasis of breast cancer to distal organs is fatal. However, few studies have identified biomarkers that are associated with distant metastatic breast cancer. Furthermore, the inability of current biomarkers, such as HER2, ER, and PR, to differentiate between distant and nondistant metastatic breast cancers accurately has necessitated the development of novel biomarker candidates.

Methods: An integrated proteomics approach that combined filter-aided sample preparation, tandem mass tag labeling (TMT), high pH fractionation, and high-resolution MS was applied to acquire in-depth proteomic data from FFPE distant metastatic breast cancer tissues. A bioinformatics analysis was performed with regard to gene ontology and signaling pathways using differentially expressed proteins (DEPs) to examine the molecular characteristics of distant metastatic breast cancer. In addition, real-time polymerase chain reaction (RT-PCR) and invasion/migration assays were performed to validate the differential regulation and function of our protein targets.

Results: A total of 9441 and 8746 proteins were identified from the pooled and individual sample sets, respectively. Based on our criteria, TUBB2A was selected as a novel biomarker candidate. The metastatic activities of TUBB2A were subsequently validated. In our bioinformatics analysis using DEPs, we characterized the overall molecular features of distant metastasis and measured differences in the molecular functions of distant metastatic breast cancer between breast cancer subtypes.

Conclusions: Our report is the first study to examine the distant metastatic breast cancer proteome using FFPE tissues. The depth of our dataset allowed us to discover a novel biomarker candidate and a proteomic characteristics of distant metastatic breast cancer. Distinct molecular features of various breast cancer subtypes were also established. Our proteomic data constitute a valuable resource for research on distant metastatic breast cancer.

Keywords: Biomarkers; Distant metastatic breast cancer; Formalin-fixed paraffin-embedded (FFPE) tissue; Quantitative proteomics; Tandem mass tag (TMT).