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HIV infection alters the human epigenetic landscape

Gene Therapy volume 26, pages 29–39 (2019)Cite this article

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Abstract

Many complex diseases or traits are the results of both genetic and environmental factors. The environmental factors affect the human body by modifying its epigenetics, which controls the activity of genomes without mutating it. Viral infection is one of the common environmental factors for complex diseases. For example, the human immunodeficiency virus (HIV) infection can cause acquired immune deficiency syndrome (AIDS), HBV, and HCV infections are associated with hepatocellular carcinoma, and human papillomavirus infection is a causal factor in cervical carcinoma. In this study, to investigate how HIV infection affects DNA methylation, we analyzed the blood DNA methylation data of 485 512 sites in 44 HIV- and 142 HIV + patients. Several advanced computational methods were applied to identify the core distinctive features that were different between the HIV patients and the healthy controls. These methods can be used for differentiating HIV-infected patients from uninfected ones. These core distinctive DNA methylation features were confirmed to be functionally connected to premature aging and abnormal immune regulation, two typical pathological symptoms of HIV infection, revealing the potential regulatory mechanisms of HIV infection on the DNA methylation status of the host cells and provided novel insights on the pathogenesis of HIV infection and AIDS.

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Funding

This study was supported by the National Natural Science Foundation of China [31701151, 31571343, 61462018], Natural Science Foundation of Shanghai [17ZR1412500, 16ZR1403100], Shanghai Sailing Program, the Youth Innovation Promotion Association of Chinese Academy of Sciences (CAS) [2016245], the fund of the key Laboratory of Stem Cell Biology of Chinese Academy of Sciences [201703], Science and Technology Commission of Shanghai Municipality (STCSM) (18dz2271000).

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Authors and Affiliations

  1. School of Life Sciences, Shanghai University, Shanghai, 200444, China

    Lei Chen & Yu-Dong Cai

  2. Shanghai Key Laboratory of PMMP, East China Normal University, Shanghai, 200241, China

    Lei Chen

  3. College of Information Engineering, Shanghai Maritime University, Shanghai, 201306, China

    Lei Chen

  4. Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark

    Shiqi Zhang

  5. Department of Medical Informatics, Erasmus MC, Rotterdam, Netherlands

    Xiaoyong Pan

  6. Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China

    XiaoHua Hu

  7. Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Yu-Hang Zhang & Tao Huang

  8. Department of Science & Technology, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, China

    Fei Yuan

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Chen, L., Zhang, S., Pan, X. et al. HIV infection alters the human epigenetic landscape. Gene Ther 26, 29–39 (2019). https://doi.org/10.1038/s41434-018-0051-6

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