Methylation changes of liver DNA during the formation of gallstones

Abstract

Aim: To explore the overall methylation changes in liver tissues during the formation of gallstones, as well as the key pathways and genes involved in the process. Methods: Reduced-representation bisulfite sequencing and RNA sequencing were conducted on the liver tissues of mice with gallstones and control normal mice. Results: A total of 8705 differentially methylated regions in CpG and 1410 differentially expressed genes were identified. The joint analysis indicated that aberrant DNA methylation may be associated with dysregulated gene expression in key pathways such as cholesterol metabolism and bile secretion. Conclusion: We propose for the first time that methylation changes in some key pathway genes in liver tissue may be involved in the formation of gallstones.

Tweetable abstract

The methylation status and downstream expression levels of many key pathways involved in gallstones formation were altered in the liver tissue of mice with gallstones.

Summary points

• Gallstones are one of the most common gastrointestinal diseases and cause huge medical costs every year around the world.

• The specific causes of gallstone formation are currently not fully understood. It is not yet known whether DNA methylation is related to the formation of gallstones.

• This study revealed the overall methylation changes in liver tissue of gallstone mice through reduced-representation bisulfite sequencing and RNA sequencing.

• A total of 8705 differentially methylated regions in CpG and 1410 differentially expressed genes were identified in the analyzed samples.

• The methylation status of genes in numerous pathways closely related to gallstone formation, including cholesterol metabolism and bile secretion, was significantly altered.

• The joint analysis of methylome and transcriptome data indicated that aberrant DNA methylation may be associated with dysregulated gene expression in key pathways such as cholesterol metabolism and bile secretion.

• In this study, we first proposed that methylation changes in some key pathways in liver tissue may be related to the formation of gallstones.

• This research result provides a new perspective for understanding the formation mechanism of gallstones.

Keywords: :

• DNA methylation
• gallstones
• gene expression
• liver
• reduced-representation bisulfite sequencing
• RNA-seq
• RRBS

Author contributions

B Cao, J Yao, J Peng: concept and design of this study. J Peng, H Li, J Hu: conducted experiments and analyzed data. J Peng, J Liu, R Wang, H Xu, X Li: collected samples. M Li, X Zhong, G Chen, D Liu: interpreted data. J Peng, J Hu: drafted the manuscript. B Cao, J Yao, F Tong, J Hu: reviewed data and proofread manuscripts. All authors participated in the revision of the manuscript and ultimately approved it.

Financial disclosure

This work was supported by the Natural Science Foundation of Anhui Province (1808085MH237), the Science Project of Education Department in Anhui Province (KJ2020A0854, KJ2021A1258, 2020jyxm0952) and the Scientific Project of Health Department in Anhui Province (2018SEYL004, AHWJ2021a010). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Competing interests disclosure

The authors have no competing interests or relevant affiliations with any organization or entity with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Writing disclosure

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

All animal experiments were approved by Biomedical Research Ethics Committee of Anhui University of Science and Technology.

Data sharing statement

The original sequencing data of this study is available in the Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra). The accession number is from SRR27755701 to SRR27755716.

Acknowledgments

The authors would like to express sincere gratitude to the staff of the Animal Experiment Center of Anhui University of Science and Technology for their assistance during the experiment.

Additional information

Funding

This work was supported by the Natural Science Foundation of Anhui Province (1808085MH237), the Science Project of Education Department in Anhui Province (KJ2020A0854, KJ2021A1258, 2020jyxm0952) and the Scientific Project of Health Department in Anhui Province (2018SEYL004, AHWJ2021a010).