S RATO¹, A RAUSELL¹, S QUENNEVILLE¹, M MUÑOZ¹, A TELENTI², A CIUFFI<sup>1

1</sup>Institute of Microbiology, University of Lausanne, Lausanne, Switzerland, ²J. Craig Venter Institute, La Jolla, USA

Cellular permissiveness to HIV infection is highly heterogeneous across individuals. Heterogeneity is also found across CD4+ T cells from the same individual, where only a fraction of cells gets infected. We used a single-cell RNA-Seq approach to investigate cellular heterogeneity and identify biomarkers of HIV permissiveness. CD4+ T cells from healthy donors were activated by TCR-mediated stimulation for three days and tested for their permissiveness to HIV infection. Non-infected activated CD4+ T cells from a highly and a poorly susceptible individual were selected and used for single-cell RNA-seq analysis using fluidigm C1 technology. RNA-Seq profiles from 85 highly permissive and 81 poorly permissive single cells were successfully obtained, with ~25 million reads per single cell. Transcriptional heterogeneity translated in a continuum of intermediary cell states in both highly and poorly permissive donor cells, which was mainly driven by TCR-mediated cell activation. Genes whose expression was differential across cells, across both donors and that encoded proteins expressed at the cell surface were further investigated as candidate biomarkers of HIV permissiveness. Single biomarkers were tested for their ability to identify permissive cells, showing enrichment in HIV infection. The combination of multiple candidate biomarkers further selected for highly permissive cells, thus defining the “HIV-permissive cell”.
Our data identified activation as a major determinant driving cellular heterogeneity in HIV permissiveness and further revealed the role of single candidate biomarkers in defining the HIV highly permissive cell.