Biol Rev Camb Philos Soc. 2018 Aug 13. doi: 10.1111/brv.12457. [Epub ahead of print]
Comprehensive review of Hepatitis B Virus-associated hepatocellular carcinoma research through text mining and big data analytics.
Lee WY1,2, Bachtiar M1,3, Choo CCS2,3, Lee CG1,2,3,4.
Author information
1
Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
2
NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119077, Singapore.
3
Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.
4
Duke-National University of Singapore Graduate Medical School, Singapore, 169547, Singapore.
Abstract
PubMed was text mined to glean insights into the role of Hepatitis B virus (HBV) in hepatocellular carcinoma (HCC) from the massive number of publications (9249) available to date. Reports from ∼70 countries identified >1300 human genes associated with either the Core, Surface or X gene in HBV-associated HCC. One hundred and forty-three of these host genes, which can potentially yield 1180 biomolecular interactions, each were reported in at least three different publications to be associated with the same HBV. These 143 genes function in 137 pathways, involved mainly in the cell cycle, apoptosis, inflammation and signalling. Fourteen of these molecules, primarily transcriptional regulators or kinases, play roles in several pathways pertinent to the hallmarks of cancers. 'Chronic' was the most frequent word used across the 9249 abstracts. A key event in chronic HBV infection is the integration of HBV into the host genome. The advent of cost-effective, next-generation sequencing technology facilitated the employment of big-data analytics comprehensively to characterize HBV-host integration within HCC patients. A total of 5331 integration events were reported across seven publications, with most of these integrations observed between the Core/X gene and the introns of genes. Nearly one-quarter of the intergenic integrations are within repeats, especially long interspersed nuclear elements (LINE) repeats. Integrations within 13 genes were each reported by at least three different studies. The human gene with the most HBV integrations observed is the TERT gene where a total of 224 integrations, primarily at its promoter and within the tumour tissue, were reported by six of seven publications. This unique review, which employs state-of-the-art text-mining and data-analytics tools, represents the most complete, systematic and comprehensive review of nearly all the publications associated with HBV-associated HCC research. It provides important resources to either focus future research or develop therapeutic strategies to target key molecules reported to play important roles in key pathways of HCC, through the systematic analyses of the commonly reported molecules associated with the various HBV genes in HCC, including information about the interactions amongst these commonly reported molecules, the pathways in which they reside as well as detailed information regarding the viral and host genes associated with HBV integration in HCC patients. Hence this review, which highlights pathways and key human genes associated with HBV in HCC, may facilitate the deeper elucidation of the role of HBV in hepato-carcinogenesis, potentially leading to timely intervention against this deadly disease.
KEYWORDS:
1
新加坡国立大学Yong Loo Lin医学院生物化学系，新加坡，119077，新加坡。
2
新加坡国立大学综合科学与工程研究生院，新加坡，119077，新加坡。
3
新加坡国立癌症中心Humphrey Oei癌症研究所医学科，新加坡11 Hospital Drive，169610，新加坡。
4
Duke-Singapore University of Singapore University Graduate School，Singapore，169547，新加坡。