Heterogeneity in NK memory stem cells after Zika virus infection using single cell approaches

Abstract Zika virus infection during pregnancy causes congenital defects such as microcephaly and ocular pathologies. Our lab previously reported that Zika virus infection in mice induces memory like NK cells that express CD27, had higher TCF-1 levels and possessed superior antiviral ability than naïve CD27+ NK cells. Moreover, these cells revealed stem like properties. We termed those NK cells with memory and stem cell like features as “NK memory stem cells (NKSCM). We hypothesized that NKSCM may contain subpopulations that differ in stemness program and antiviral capacity. To determine this, we performed single cell RNA-seq on NKSCM cells. Our analysis revealed 8 distinct clusters in NKSCM. Of these, Cluster 0 showed upregulation of Dusp1, Dusp2, Junb, Fosb while cluster 4 showed downregulation of Dusp1, Dusp2, Junb, Fosb genes. Cluster 5 had upregulation of proliferation associated genes (Mki67, Cdk1 and Pcna). Cluster 3 revealed downregulation of cytotoxic genes (Prf1, Gzma, Gzmb) while gene upregulation of Id3, Myb, Sell, Cd226 and Cxcr3 was evident in this subset. Similarly, other clusters showed differential gene expression profiles. Currently, our analysis is ongoing for single cell ATAC-seq datasets to determine epigenome at single cell level in these NKSCM clusters. Finally, the experiments are underway to functionally characterize these NKSCM subpopulations and to evaluate their role in Zika viral defense. This work was supported by Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, TX, USA and American Association of Immunology Careers in Immunology Fellowship