Altered cfDNA fragmentation profile in hypomethylated regions as diagnostic markers in breast cancer

Jun Wang; Yanqin Niu; Ming Yang; Lirong Shu; Hongxian Wang; Xiaoqian Wu; Yaqin He; Peng Chen; Guocheng Zhong; Zhixiong Tang; Shasha Zhang; Qianwen Guo; Yun Wang; Li Yu; Deming Gou

doi:10.1186/s13072-023-00508-4

Altered cfDNA fragmentation profile in hypomethylated regions as diagnostic markers in breast cancer

Epigenetics Chromatin. 2023 Sep 23;16(1):33. doi: 10.1186/s13072-023-00508-4.

Authors

Jun Wang¹, Yanqin Niu¹, Ming Yang¹, Lirong Shu¹, Hongxian Wang², Xiaoqian Wu², Yaqin He³, Peng Chen¹, Guocheng Zhong⁴, Zhixiong Tang¹, Shasha Zhang¹, Qianwen Guo¹, Yun Wang¹, Li Yu⁴, Deming Gou⁵

Affiliations

¹ Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China.
² Department of Thyroid and Breast, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518052, China.
³ Surgical Department, General Hospital of Ningxia Medical University, Yinchuan, 750003, China.
⁴ Department of Hematology and Oncology, Shenzhen University General Hospital, Carson International Cancer Research Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China.
⁵ Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China. dmgou@szu.edu.cn.

Abstract

Background: Breast cancer, the most common malignancy in women worldwide, has been proven to have both altered plasma cell-free DNA (cfDNA) methylation and fragmentation profiles. Nevertheless, simultaneously detecting both of them for breast cancer diagnosis has never been reported. Moreover, although fragmentation pattern of cfDNA is determined by nuclease digestion of chromatin, structure of which may be affected by DNA methylation, whether cfDNA methylation and fragmentation are biologically related or not still remains unclear.

Methods: Improved cfMeDIP-seq were utilized to characterize both cfDNA methylation and fragmentation profiles in 49 plasma samples from both healthy individuals and patients with breast cancer. The feasibility of using cfDNA fragmentation profile in hypo- and hypermethylated regions as diagnostic markers for breast cancer was evaluated.

Results: Mean size of cfDNA fragments (100-220 bp) mapped to hypomethylated regions decreased more in patients with breast cancer (4.60 bp, 172.33 to 167.73 bp) than in healthy individuals (2.87 bp, 174.54 to 171.67 bp). Furthermore, proportion of short cfDNA fragments (100-150 bp) in hypomethylated regions when compared with it in hypermethylated regions was found to increase more in patients with breast cancer in two independent discovery cohort. The feasibility of using abnormality of short cfDNA fragments ratio in hypomethylated genomic regions for breast cancer diagnosis in validation cohort was evaluated. 7 out of 11 patients were detected as having breast cancer (63.6% sensitivity), whereas no healthy individuals were mis-detected (100% specificity).

Conclusion: We identified enriched short cfDNA fragments after 5mC-immunoprecipitation (IP) in patients with breast cancer, and demonstrated the enriched short cfDNA fragments might originated from hypomethylated genomic regions. Furthermore, we proved the feasibility of using differentially methylated regions (DMRs)-dependent cfDNA fragmentation profile for breast cancer diagnosis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Breast Neoplasms* / diagnosis
Breast Neoplasms* / genetics
Cell-Free Nucleic Acids* / genetics
Chromatin
DNA Methylation
Female
Genomics
Humans

Substances

Cell-Free Nucleic Acids
Chromatin