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ORIGINAL RESEARCH article
Front. Pharmacol.
Sec. Pharmacology of Anti-Cancer Drugs
Volume 15 - 2024 |
doi: 10.3389/fphar.2024.1465586
This article is part of the Research Topic Advancements in the Heterogeneity of Sex for Tumors View all 5 articles
Analysis of chromatin accessibility in peripheral blood mononuclear cells from early-stage breast cancer patients
Provisionally accepted- 1 Department of Cosmetology and Plastic Surgery Center, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- 2 Guangzhou First People's Hospital, Guangzhou, Guangdong Province, China
- 3 The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
- 4 Department of Cosmetology and Plastic Surgery Center, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
- 5 The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
Objective: To explore the specific open region of chromatin in peripheral blood mononuclear cells (PBMC) of breast cancer patients and explore its possibility as biomarkers for diagnosis and predicting prognosis of breast cancer. Methods: We obtained PBMCs from breast cancer patients and healthy population for ATAC-seq (n=3), and obtained GSE27562 chip sequencing data sequencing for secondary analysis. Through bioinformatics analysis, we mined the change pattern of chromatin accessibility in PBMC of breast cancer. Results: A total of 1906 differentially accessible regions (DAR) and 1632 differentially expressed genes (DEGs) were identified in ATAC sequencing. Upregulated DEG in the disease group is mainly distributed in cells, organelles and cell intima related structures, mainly performing biological functions such as cell nitrogen complex metabolism, macromolecular metabolism and cell communication, and also related to functions such as nucleic acid binding, enzyme binding, hydrolase reaction and transferase activity. Combined with the microarray data analysis, the latter set of nine DEGs showed intersection in ATAC and microarray data, including Jun, MSL 2, CDC42, TRIB 1, SERTAD3, RAB 14, RHOB, RAB40B, and PRKDC. HOMER predicted identified five transcription factors potentially binding to these Peak sites, including NFY, Sp 2, GFY, NRF, and ELK 1. Conclusion: Chromatin accessibility analysis of peripheral blood mononuclear cells in early breast cancer patients underscores its potential as a significant avenue for biomarker discovery in breast cancer diagnostics and treatment. By screening transcription factors and differentially expressed genes related to breast cancer, this research provides a comprehensive theoretical foundation that may guide future clinical applications and therapeutic developments.
Keywords: breast cancer, detection of peripheral blood mononuclear cells (PBMC), chromatin transposase sequencing, transcription factor, ATAC-seq
Received: 16 Jul 2024; Accepted: 27 Aug 2024.
Copyright: © 2024 Xia, Lu, Qin, Huang, Kong and Deng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Longjie Xia, Department of Cosmetology and Plastic Surgery Center, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
Yixuan Qin, Department of Cosmetology and Plastic Surgery Center, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
Runchun Huang, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
Fanbiao Kong, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, Nanning, China
Yu Deng, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, Guangdong Province, China
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