Functional and transcriptional heterogeneity within the massively expanding HLADR + CD38 + CD8 T cell population in acute febrile dengue patients

Abstract

ABSTRACT CD8 T cells are important tools for protection against intracellularly replicating pathogens such as viruses. Previous studies showed that a discrete population of HLADR and CD38-expressing CD8 T cells expands massively during the acute febrile phase of human dengue virus infection—but very few of these cells secrete IFNγ upon in vitro stimulation with dengue peptides. To gain a better understanding of what other cytokines/chemokines do these massively expanding HLADR + CD38 + CD8 T cells express, we performed RNA seq of sorted HLADR + CD38 + CD8 T cell subsets after peptide stimulation. A majority of these peptide-stimulated HLADR + CD38 + CD8 T cells were CD69 - IFNγ - , nearly a third were CD69 + IFNγ - , whereas very few (<10%) were CD69 + IFNγ + . The CD69 - IFNγ - subset was enriched for the expression of key genes implicated in the negative regulation of T cell receptor (TCR) signaling and T-cell exhaustion, attraction of B cells and other lymphocytes, and cytokines related to Tc17/T-reg lineages or those that are implicated in immunosuppression/immunomodulatory and anti-inflammatory activities and angiogenesis. The CD69 + IFNγ - subset showed enriched transcription of key genes implicated in cytotoxic effector functions as well as costimulatory and signaling adaptors implicated in fine balancing of T cell receptor signaling. The CD69 + IFNγ + subset largely shared the transcriptional profile with the CD69 + IFNγ - subset—but with relatively more pronounced expression along with additional genes such as chemokines XCL1/XCL2. Our findings showing distinct functional subsets among these massively expanding CD8 T cells in dengue CD8 T cells warrant further studies to carefully examine the precise role of these T cell subsets in protection against dengue. IMPORTANCE CD8 T cells play a crucial role in protecting against intracellular pathogens such as viruses by eliminating infected cells and releasing anti-viral cytokines such as interferon gamma (IFNγ). Consequently, there is significant interest in comprehensively characterizing CD8 T cell responses in acute dengue febrile patients. Previous studies, including our own, have demonstrated that a discrete population of CD8 T cells with HLADR + CD38 + phenotype undergoes massive expansion during the acute febrile phase of natural dengue virus infection. Although about a third of these massively expanding HLADR + CD38 + CD8 T cells were also CD69 high when examined ex vivo , only a small fraction of them produced IFNγ upon in vitro peptide stimulation. Therefore, to better understand such functional diversity of CD8 T cells responding to dengue virus infection, it is important to know the cytokines/chemokines expressed by these peptide-stimulated HLADR + CD38 + CD8 T cells and the transcriptional profiles that distinguish the CD69 + IFNγ + , CD69 + IFNγ - , and CD69 - IFNγ - subsets.