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Erratum published on 2 May 2019, see Genes 2019, 10(5), 335.
Open AccessArticle

Low-Grade Dysplastic Nodules Revealed as the Tipping Point during Multistep Hepatocarcinogenesis by Dynamic Network Biomarkers

by Lina Lu 1,†, Zhonglin Jiang 1,†, Yulin Dai 2 and Luonan Chen 1,3,*
1
Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
2
Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, Houston, TX 77030, USA
3
School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2017, 8(10), 268; https://doi.org/10.3390/genes8100268
Received: 29 July 2017 / Revised: 26 September 2017 / Accepted: 1 October 2017 / Published: 13 October 2017
(This article belongs to the Special Issue Integrative Genomics and Systems Medicine in Cancer)
Hepatocellular carcinoma (HCC) is a complex disease with a multi-step carcinogenic process from preneoplastic lesions, including cirrhosis, low-grade dysplastic nodules (LGDNs), and high-grade dysplastic nodules (HGDNs) to HCC. There is only an elemental understanding of its molecular pathogenesis, for which a key problem is to identify when and how the critical transition happens during the HCC initiation period at a molecular level. In this work, for the first time, we revealed that LGDNs is the tipping point (i.e., pre-HCC state rather than HCC state) of hepatocarcinogenesis based on a series of gene expression profiles by a new mathematical model termed dynamic network biomarkers (DNB)—a group of dominant genes or molecules for the transition. Different from the conventional biomarkers based on the differential expressions of the observed genes (or molecules) for diagnosing a disease state, the DNB model exploits collective fluctuations and correlations of the observed genes, thereby predicting the imminent disease state or diagnosing the critical state. Our results show that DNB composed of 59 genes signals the tipping point of HCC (i.e., LGDNs). On the other hand, there are a large number of differentially expressed genes between cirrhosis and HGDNs, which highlighted the stark differences or drastic changes before and after the tipping point or LGDNs, implying the 59 DNB members serving as the early-warning signals of the upcoming drastic deterioration for HCC. We further identified the biological pathways responsible for this transition, such as the type I interferon signaling pathway, Janus kinase–signal transducers and activators of transcription (JAK–STAT) signaling pathway, transforming growth factor (TGF)-β signaling pathway, retinoic acid-inducible gene I (RIG-I)-like receptor signaling pathway, cell adhesion molecules, and cell cycle. In particular, pathways related to immune system reactions and cell adhesion were downregulated, and pathways related to cell growth and death were upregulated. Furthermore, DNB was validated as an effective predictor of prognosis for HCV-induced HCC patients by survival analysis on independent data, suggesting a potential clinical application of DNB. This work provides biological insights into the dynamic regulations of the critical transitions during multistep hepatocarcinogenesis. View Full-Text
Keywords: dynamic network biomarkers; hepatocellular carcinoma; low-grade dysplastic nodules; tipping point dynamic network biomarkers; hepatocellular carcinoma; low-grade dysplastic nodules; tipping point
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Lu, L.; Jiang, Z.; Dai, Y.; Chen, L. Low-Grade Dysplastic Nodules Revealed as the Tipping Point during Multistep Hepatocarcinogenesis by Dynamic Network Biomarkers. Genes 2017, 8, 268.

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