Novel lncRNAs with diagnostic or prognostic value screened out from breast cancer via bioinformatics analyses

PeerJ

article

Hongxian Wang¹  Lirong Shu²  Nan Niu²  Chenyang Zhao²  Shuqi Lu²  Yanhua Li¹  Huanyu Wang¹  Yao Liu¹  Tianhui Zou¹  Jiawei Zou¹  Xiaoqin Wu¹  Yun Wang² 

[1] Department of Thyroid and Breast Surgery, Shenzhen Nanshan People’s Hospital and the 6th Affiliated Hospital of Shenzhen University;Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University

关键词: Breast cancer;    Exosome;    lncRNA;    Biomarker;    Diagnosis;    Prognosis;   

DOI  :  10.7717/peerj.13641

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundRecent studies have shown that long non-coding RNAs (lncRNAs) may play key regulatory roles in many malignant tumors. This study investigated the use of novel lncRNA biomarkers in the diagnosis and prognosis of breast cancer.Materials and MethodsThe database subsets of The Cancer Genome Atlas (TCGA) by RNA-seq for comparing analysis of tissue samples between breast cancer and normal control groups were downloaded. Additionally, anticoagulant peripheral blood samples were collected and used in this cohort study. The extracellular vesicles (EVs) from the plasma were extracted and sequenced, then analyzed to determine the expressive profiles of the lncRNAs, and the cancer-related differentially expressed lncRNAs were screened out. The expressive profiles and associated downstream-mRNAs were assessed using bioinformatics (such as weighted correlation network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichments, Receiver-Operating Characteristic (ROC) curve and survival analysis, etc.) to investigate the diagnostic and prognostic values of these EV lncRNAs and their effectors.Results70%, indicating that the combined one has a good diagnostic value. In addition, the results of survival analysis suggested that two lncRNAs with low expressive levels may indicate the poor prognosis of breast cancer. By tissue sample verification, C15orf54, AL157935.1, LINC01117, and SNHG3 were determined to have good diagnostic ability in breast cancer lesions, however, there was no significant difference in the plasma EVs of patients. Moreover, survival analysis data also showed that AL355974.2 may serve as an independent prognostic factor and as a protective factor.ConclusionA total of five lncRNAs found in this study could be developed as biomarkers for breast cancer patients, including four diagnostic markers (C15orf54, AL157935.1, LINC01117, and SNHG3) and a potential prognostic marker (AL355974.2).

【 授权许可】

CC BY