Single-cell transcriptome analysis of CD34+stem cell-derived myeloid cells identifies a CFU-GEMM-like population permissive to human cytomegalovirus infection

ABSTRACTMyeloid cells are important sites of lytic and latent infection by human cytomegalovirus (CMV). We previously showed that only a small subset of myeloid cells differentiated from CD34+hematopoietic stem cells is permissive to CMV replication, underscoring the heterogeneous nature of these populations. The exact identity of susceptible and resistant cell types, and the cellular features characterizing permissive cells, however, could not be dissected using averaging transcriptional analysis tools such as microarrays and, hence, remained enigmatic. Here, we profile the transcriptomes of ∼ 7000 individual cells at day one post-infection using the 10X genomics platform. We show that viral transcripts are detectable in the majority of the cells, suggesting that virion entry is unlikely to be the main target of cellular restriction mechanisms. We further show that viral replication occurs in a small but specific sub-group of cells transcriptionally related to, and likely derived from, a cluster of cells expressing markers of Colony Forming Unit – Granulocyte, Erythrocyte, Monocyte, Megakaryocyte (CFU-GEMM) oligopotent progenitors. Compared to the remainder of the population, CFU-GEMM cells are enriched in transcripts with functions in mitochondrial energy production, cell proliferation, RNA processing and protein synthesis, and express similar or higher levels of interferon-related genes. While expression levels of the former are maintained in infected cells, the latter are strongly down-regulated. We thus propose that the preferential infection of CFU-GEMM cells may be due to the presence of a pre-established pro-viral environment, requiring minimal optimization efforts from viral effectors, rather than to the absence of specific restriction factors. Together, these findings identify a potentially new population of myeloid cells susceptible to CMV replication, and provide a possible rationale for their preferential infection.AUTHOR SUMMARYMyeloid cells such as monocytes and dendritic cells are critical targets of CMV infection. To identify the cellular factors that confer susceptibility or resistance to infection, we profiled the transcriptomes of ∼ 7,000 single cells from a population of semi-permissive myeloid cells infected with CMV. We found that viral RNAs are detectable in the majority of the cells, but that marked expression of CMV lytic genes occurs in only a small subset of cells transcriptionally related to a cluster of CFU-GEMM progenitors that express similar amounts of transcripts encoding interferon-related anti-viral factors as the rest of the population but higher levels of transcripts encoding proteins required for energy, RNA, and protein production. We thus conclude that the preferential infection of CFU-GEMM cells might be due to the pre-existing presence of an intracellular environment conducive to infection onset, rather than to the absence of anti-viral factors restricting viral entry or initial gene expression. Together, these findings uncover a new type of myeloid cells potentially permissive to CMV infection, expand our understanding of the cellular requirements for successful initiation of CMV infection, and provide new pro- and anti-viral gene candidates for future analyses and therapeutic interventions.