Novel Urine Cell-Free DNA Methylation Markers for Hepatocellular Carcinoma

Authors

Selena Lin
Wei Xia
Amy Kim
Dion Chen
Shelby Schleyer
Lin Choi
Zhili Wang
James Hamilton
Harry Luu
Hie-Won Hann, Thomas Jefferson UniversityFollow
Ting-Tsung Chang
Chi-Tan Hu
Abashai Woodard
Terence Gade
Ying-Hsiu Su

Document Type

Article

Publication Date

12-7-2023

Comments

This article is the author's final published version in Scientific Reports, Volume 13, Issue 1, December 2023, Article number 21585.

The published version is available at https://doi.org/10.1038/s41598-023-48500-y.

Copyright © The Author(s) 2023

Abstract

An optimized hepatocellular carcinoma (HCC)-targeted methylation next generation sequencing assay was developed to discover HCC-associated methylation markers directly from urine for HCC screening. Urine cell-free DNA (ucfDNA) isolated from a discovery cohort of 31 non-HCC and 30 HCC was used for biomarker discovery, identifying 29 genes with differentially methylated regions (DMRs). Methylation-specific qPCR (MSqPCR) assays were developed to verify the selected DMRs corresponding to 8 genes (GRASP, CCND2, HOXA9, BMP4, VIM, EMX1, SFRP1, and ECE). Using archived ucfDNA, methylation of GRASP, HOXA9, BMP4, and ECE1, were found to be significantly different (p < 0.05) between HCC and non-HCC patients. The four markers together with previously reported GSTP1 and RASSF1A markers were assessed as a 6-marker panel in an independent training cohort of 87 non-HCC and 78 HCC using logistic regression modeling. AUROC of 0.908 (95% CI, 0.8656-0.9252) was identified for the 6-marker panel with AFP, which was significantly higher than AFP-alone (AUROC 0.841 (95% CI, 0.778-0.904), p = 0.0026). Applying backward selection method, a 4-marker panel was found to exhibit similar performance to the 6-marker panel with AFP having 80% sensitivity compared to 29.5% by AFP-alone at a specificity of 85%. This study supports the potential use of methylated transrenal ucfDNA for HCC screening.

Recommended Citation

Lin, Selena; Xia, Wei; Kim, Amy; Chen, Dion; Schleyer, Shelby; Choi, Lin; Wang, Zhili; Hamilton, James; Luu, Harry; Hann, Hie-Won; Chang, Ting-Tsung; Hu, Chi-Tan; Woodard, Abashai; Gade, Terence; and Su, Ying-Hsiu, "Novel Urine Cell-Free DNA Methylation Markers for Hepatocellular Carcinoma" (2023). Division of Gastroenterology and Hepatology Faculty Papers. Paper 94.
https://jdc.jefferson.edu/gastro_hepfp/94

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 License.

PubMed ID

38062093

Language

English