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Proteomic profiling of HIV-1 infection of human CD4+ T cells identifies PSGL-1 as an HIV restriction factor

Nature Microbiology volume 4, pages 813–825 (2019)Cite this article

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Abstract

Human immunodeficiency virus (HIV) actively modulates the protein stability of host cells to optimize viral replication. To systematically examine this modulation in HIV infection, we used isobaric tag-based mass spectrometry to quantify changes in the abundance of over 14,000 proteins during HIV-1 infection of human primary CD4+ T cells. We identified P-selectin glycoprotein ligand 1 (PSGL-1) as an HIV-1 restriction factor downregulated by HIV-1 Vpu, which binds to PSGL-1 and induces its ubiquitination and degradation through the ubiquitin ligase SCFβ-TrCP2. PSGL-1 is induced by interferon-γ in activated CD4+ T cells to inhibit HIV-1 reverse transcription and potently block viral infectivity by incorporating in progeny virions. This infectivity block is antagonized by Vpu via PSGL-1 degradation. We further show that PSGL-1 knockdown can significantly abolish the anti-HIV activity of interferon-γ in primary CD4+ T cells. Our study identifies an HIV restriction factor and a key mediator of interferon-γ’s anti-HIV activity.

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Fig. 1: Proteomic profiling of HIV-1 infection in human primary CD4+ T cells.
Fig. 2: Comparison of proteomic profiling results with other large data sets for cross-validation and identification of candidate genes.
Fig. 3: PSGL-1 is degraded by HIV-1 via ubiquitination by the Vpu-hijacked SCFβ-TrCP2 E3 ligase.
Fig. 4: PSGL-1 in target cells inhibits HIV-1 replication, starting from DNA synthesis.
Fig. 5: PSGL-1 in producer cells inhibits the infectivity of HIV-1 progeny virions.
Fig. 6: PSGL-1 mediates the anti-HIV activity of IFN-γ in activated primary CD4+ T cells.

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Code availability

The computational code used in this study is available from the corresponding authors upon request.

Data availability

The data that support the findings of this study are available from the corresponding authors upon request. The raw proteomic data have been uploaded to the ProteomeXchange data repository with the ID number: PXD011233.

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Acknowledgements

This work was supported by grants from the State Key Research Development Program of China to X.T. (no. 2016YFC1200303) and F.Z. (no. 2017YFA0505100), the China National Funds for Excellent Young Scientists (no. 31722030), grants from the National Natural Science Foundation of China to X.-F.Y. (no. 81772169) and F.Z. (no. 31670836), a grant from the Shanghai Institute of Higher Learning to F.Z. (no. TP2015003) and a grant from the NIMH, US Public Health Service to Y.W. (no. 5R01MH102144). We thank Q. Wang and X. Ye (Institute of Microbiology of the Chinese Academy of Sciences) for the use of the Biosafety level 3 Tissue Culture Facility. We thank H. Qi, N. Yan, H. Deng, A. Elia and N. Zheng for critical reading of the manuscript.

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Author notes

  1. These authors contributed equally: Ying Liu, Yajing Fu.

Authors and Affiliations

  1. MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Advanced Innovation Center for Structural Biology, School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China

    Ying Liu, Chunyan Fu, Hang Zhang, Shuo Li, Tengjiang Zhang, Jing Gong, Xiaohui Kong & Xu Tan

  2. Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China

    Yajing Fu

  3. School of System Biology, George Mason University, Manassas, VA, USA

    Yajing Fu, Zheng Zhou, Deemah Dabbagh & Yuntao Wu

  4. Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education and Institutes of Biomedical Sciences, Fudan University, Shanghai, China

    Qian Wang & Feng Zhou

  5. Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

    Mushan Li & Zhen Shao

  6. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China

    Weiwei Zhai

  7. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China

    Weiwei Zhai

  8. Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China

    Jiaming Su & Xiao-Fang Yu

  9. Beijing You’an Hospital, Capital Medical University, Beijing, China

    Jianping Sun & Yonghong Zhang

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Contributions

X.T. conceived and supervised the project. F.Z. conducted the mass spectrometry experiment and data analysis. Y.L. conducted most of the experiments with help from C.F., H.Z., S.L., T.Z. and X.K. Y.F., Z.Z. and D.D. conducted experiments on PSGL-1-blocking viral infectivity and western blot detection of PSGL-1 in virions. Y.W. supervised experiments on PSGL-1-blocking viral infectivity. J.Su and X.-F.Y. contributed to supervision and data analysis of the project. J.Sun and Y.Z. contributed key reagents and performed clinical analysis of the study. Q.W., J.G., M.L., W.Z. and Z.S. contributed to the data analysis. X.T. and F.Z. wrote and Y.W. edited the manuscript.

Corresponding authors

Correspondence to Feng Zhou, Yuntao Wu or Xu Tan.

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Supplementary information

Supplementary Information

Supplementary Figures 1–6, Supplementary Table 1 and legends for Supplementary Datasets.

Reporting Summary

Supplementary Dataset 1

Raw mass spectrometry intensities of all identified proteins.

Supplementary Dataset 2

List of proteins with differential abundances among cell populations.

Supplementary Dataset 3

Gene ontology analysis of proteins with differential abundances among cell populations.

Supplementary Dataset 4

List of interferon-stimulated genes.

Supplementary Dataset 5

List of read counts of RNA-seq analysis.

Supplementary Dataset 6

List of genes with differential mRNA levels among cell populations.

Supplementary Dataset 7

List of positively selected genes.

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Liu, Y., Fu, Y., Wang, Q. et al. Proteomic profiling of HIV-1 infection of human CD4+ T cells identifies PSGL-1 as an HIV restriction factor. Nat Microbiol 4, 813–825 (2019). https://doi.org/10.1038/s41564-019-0372-2

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