Identification of novel HIV-1 dependency factors in primary CCR4(+)CCR6(+)Th17 cells via a genome-wide transcriptional approach

Retrovirology. 2015 Dec 10;12:102. doi: 10.1186/s12977-015-0226-9.

Abstract

Background: The HIV-1 infection is characterized by profound CD4(+) T cell destruction and a marked Th17 dysfunction at the mucosal level. Viral suppressive antiretroviral therapy restores Th1 but not Th17 cells. Although several key HIV dependency factors (HDF) were identified in the past years via genome-wide siRNA screens in cell lines, molecular determinants of HIV permissiveness in primary Th17 cells remain to be elucidated.

Results: In an effort to orient Th17-targeted reconstitution strategies, we investigated molecular mechanisms of HIV permissiveness in Th17 cells. Genome-wide transcriptional profiling in memory CD4(+) T-cell subsets enriched in cells exhibiting Th17 (CCR4(+)CCR6(+)), Th1 (CXCR3(+)CCR6(-)), Th2 (CCR4(+)CCR6(-)), and Th1Th17 (CXCR3(+)CCR6(+)) features revealed remarkable transcriptional differences between Th17 and Th1 subsets. The HIV-DNA integration was superior in Th17 versus Th1 upon exposure to both wild-type and VSV-G-pseudotyped HIV; this indicates that post-entry mechanisms contribute to viral replication in Th17. Transcripts significantly enriched in Th17 versus Th1 were previously associated with the regulation of TCR signaling (ZAP-70, Lck, and CD96) and Th17 polarization (RORγt, ARNTL, PTPN13, and RUNX1). A meta-analysis using the NCBI HIV Interaction Database revealed a set of Th17-specific HIV dependency factors (HDFs): PARG, PAK2, KLF2, ITGB7, PTEN, ATG16L1, Alix/AIP1/PDCD6IP, LGALS3, JAK1, TRIM8, MALT1, FOXO3, ARNTL/BMAL1, ABCB1/MDR1, TNFSF13B/BAFF, and CDKN1B. Functional studies demonstrated an increased ability of Th17 versus Th1 cells to respond to TCR triggering in terms of NF-κB nuclear translocation/DNA-binding activity and proliferation. Finally, RNA interference studies identified MAP3K4 and PTPN13 as two novel Th17-specific HDFs.

Conclusions: The transcriptional program of Th17 cells includes molecules regulating HIV replication at multiple post-entry steps that may represent potential targets for novel therapies aimed at protecting Th17 cells from infection and subsequent depletion in HIV-infected subjects.

Publication types

  • Meta-Analysis

MeSH terms

  • Adult
  • Cells, Cultured
  • Female
  • Gene Expression Profiling
  • HIV Infections / virology*
  • HIV-1 / physiology*
  • Humans
  • Immunity, Mucosal
  • Immunologic Memory
  • MAP Kinase Kinase Kinase 4 / genetics
  • MAP Kinase Kinase Kinase 4 / metabolism
  • Male
  • NF-kappa B / metabolism
  • Protein Tyrosine Phosphatase, Non-Receptor Type 13 / genetics
  • Protein Tyrosine Phosphatase, Non-Receptor Type 13 / metabolism
  • RNA Interference
  • Receptors, Antigen, T-Cell / genetics
  • Receptors, Antigen, T-Cell / immunology*
  • Receptors, Antigen, T-Cell / metabolism
  • Receptors, CCR4 / immunology
  • Receptors, CCR6 / immunology
  • T-Lymphocyte Subsets / virology
  • Th1 Cells / immunology
  • Th1 Cells / virology
  • Th17 Cells / classification
  • Th17 Cells / immunology*
  • Th17 Cells / virology*
  • Transcriptome
  • Virus Replication*

Substances

  • CCR4 protein, human
  • CCR6 protein, human
  • NF-kappa B
  • Receptors, Antigen, T-Cell
  • Receptors, CCR4
  • Receptors, CCR6
  • MAP Kinase Kinase Kinase 4
  • PTPN13 protein, human
  • Protein Tyrosine Phosphatase, Non-Receptor Type 13