Collagen proteins, thrombospondin 1 and lumican are differentially expressed across breast cancer subtypes by functional proteomics from core needle biopsy samples of Taiwanese breast cancer

IF 2.2 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports Pub Date : 2025-08-31 DOI:10.1016/j.bbrep.2025.102210

Wei-Chi Ku , Nam Nhut Phan , Chih-Yi Liu , Chi-Jung Huang , Chen-Chung Liao , Yen-Chun Huang , Po-Hsin Kong , Ling-Ming Tseng , Chi-Cheng Huang

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引用次数: 0

Abstract

Purpose

This study aimed to conduct functional proteomics across breast cancer subtypes with bioinformatics analyses.

Methods

Candidate proteins were identified using nanoscale liquid chromatography with tandem mass spectrometry (NanoLC-MS/MS) from core needle biopsy samples of early stage (0-III) breast cancers, followed by external validation with public domain gene-expression datasets (TCGA TARGET GTEx and TCGA BRCA).

Results

Seventeen proteins demonstrated significantly differential expression and protein-protein interaction (PPI) found the strong networks including COL2A1, COL11A1, COL6A1, COL6A2, THBS1 and LUM. Public domain databases also showed that COL2A1, COL11A1, COL6A1, COL6A2 and LUM were higher in primary/metastatic tumor than in normal tissue (one-way ANOVA, all P-values less than 0.001), and all six genes were differentially expressed across four molecular subtypes based on hormone receptor (HR) status and human epidermal growth factor receptor II (HER2) status (one-way ANOVA, all P-values less than 0.001). Disease-specific survival discrepancy was observed comparing breast cancer patients of the upper and lower quartile of the collagen family (COL2A1, COL11A1, COL6A1, COL6A2), THBS1 and LUM gene expression signature (log-rank test, P = 0.06).

Conclusion

Functional proteomics suggested that collagen proteins, thrombospondin 1 and lumican are differentially expressed across breast cancer subtypes.

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台湾乳腺癌核心针活检样本的功能蛋白质组学研究发现，胶原蛋白、血小板反应蛋白1和lumican在乳腺癌亚型中的表达存在差异

目的通过生物信息学分析对乳腺癌亚型进行功能蛋白质组学研究。方法采用纳米级液相色谱串联质谱法（NanoLC-MS/MS）从早期（0-III期）乳腺癌核心针活检样本中鉴定候选蛋白，然后使用公共领域基因表达数据集（TCGA TARGET GTEx和TCGA BRCA）进行外部验证。结果17个蛋白存在显著的差异表达，其中COL2A1、COL11A1、COL6A1、COL6A2、THBS1和LUM具有较强的蛋白相互作用网络。公共领域数据库还显示，COL2A1、COL11A1、COL6A1、COL6A2和LUM在原发性/转移性肿瘤中的表达高于正常组织（单因素方差分析，所有p值均小于0.001），并且基于激素受体（HR）状态和人表皮生长因子受体II （HER2）状态，所有6个基因在4种分子亚型中表达差异（单因素方差分析，所有p值均小于0.001）。比较胶原蛋白家族（COL2A1、COL11A1、COL6A1、COL6A2）、THBS1和LUM基因表达特征的上、下四分位数乳腺癌患者的疾病特异性生存差异（log-rank检验，P = 0.06）。结论功能蛋白质组学提示胶原蛋白、血小板反应蛋白1和lumican在不同乳腺癌亚型中的表达存在差异。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Biochemistry and Biophysics Reports Biochemistry, Genetics and Molecular Biology-Biophysics

CiteScore

4.60

自引率

0.00%

发文量

191

审稿时长

59 days

期刊介绍： Open access, online only, peer-reviewed international journal in the Life Sciences, established in 2014 Biochemistry and Biophysics Reports (BB Reports) publishes original research in all aspects of Biochemistry, Biophysics and related areas like Molecular and Cell Biology. BB Reports welcomes solid though more preliminary, descriptive and small scale results if they have the potential to stimulate and/or contribute to future research, leading to new insights or hypothesis. Primary criteria for acceptance is that the work is original, scientifically and technically sound and provides valuable knowledge to life sciences research. We strongly believe all results deserve to be published and documented for the advancement of science. BB Reports specifically appreciates receiving reports on: Negative results, Replication studies, Reanalysis of previous datasets.