meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data

Wu, Qiong1,2,3; Zheng, Xubin1,4; Leung, Kwong-Sak4; Wong, Man-Hon4; Tsui, Stephen Kwok-Wing2; Cheng, Lixin1

2022-06-01

10.1093/bioinformatics/btac379

BIOINFORMATICS   Impact Factor & Quartile

1367-4803

1460-2059

["Motivation: Hepatocellular carcinoma (HCC) is a primary malignancy with a poor prognosis. Recently, multi-omics molecular-level measurement enables HCC diagnosis and prognosis prediction, which is crucial for early intervention of personalized therapy to diminish mortality. Here, we introduce a novel strategy utilizing DNA methylation and RNA expression data to achieve a multi-omics gene pair signature (GPS) for HCC discrimination.","Results: The immune genes with negative correlations between expression and promoter methylation are enriched in the highly connected cancer-related pathway network, which are considered as the candidates for HCC detection. After that, we separately construct a methylation GPS (mGPS) and an expression GPS (eGPS), and then assemble them as a meGPS with five gene pairs, in which the significant methylation and expression changes occur between HCC tumor and non-tumor groups. Reliable performance has been validated by independent tissue (age, gender and etiology) and blood datasets. This study proposes a procedure for multi-omics GPS identification and develops a novel HCC signature using both methylome and transcriptome data, suggesting potential molecular targets for the detection and therapy of HCC."]

SCI

English

First ; Corresponding

Guangdong Basic and Applied Basic Research Foundation[2019A1515110097] ; General Research Fund of the Hong Kong Research Grants Council[14175617,14119420,14119219] ; Health and Medical Research Fund of the Food and Health Bureau of the Hong Kong Special Administrative Region government["06171016","07181266"]

Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics

Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability

WOS:000809396400001

OXFORD UNIV PRESS

BIOLOGY & BIOCHEMISTRY

Web of Science

1.Jinan Univ, Clin Med Coll 2, Southern Univ Sci & Technol, Affiliated Hosp 1,Shenzhen Peoples Hosp, Shenzhen 518020, Peoples R China
2.Chinese Univ Hong Kong, Sch Biomed Sci, Hong Kong, Peoples R China
3.Chinese Univ Hong Kong, Prince Wales Hosp, Dept Paediat, Hong Kong, Peoples R China
4.Chinese Univ Hong Kong, Dept Comp Sci & Engn, Hong Kong, Peoples R China

Wu, Qiong,Zheng, Xubin,Leung, Kwong-Sak,et al. meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data[J]. BIOINFORMATICS,2022.

Wu, Qiong,Zheng, Xubin,Leung, Kwong-Sak,Wong, Man-Hon,Tsui, Stephen Kwok-Wing,&Cheng, Lixin.(2022).meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data.BIOINFORMATICS.

Wu, Qiong,et al."meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data".BIOINFORMATICS (2022).