Temporally integrated single cell RNA sequencing analysis of PBMC from experimental and natural primary human DENV-1 infections

Abstract

Dengue human infection studies present an opportunity to address many longstanding questions in the field of flavivirus biology. However, limited data are available on how the immunological and transcriptional response elicited by an attenuated challenge virus compares to that associated with a wild-type DENV infection. To determine the kinetic transcriptional signature associated with experimental primary DENV-1 infection and to assess how closely this profile correlates with the transcriptional signature accompanying natural primary DENV-1 infection, we utilized scRNAseq to analyze PBMC from individuals enrolled in a DENV-1 human challenge study and from individuals experiencing a natural primary DENV-1 infection. While both experimental and natural primary DENV-1 infection resulted in overlapping patterns of inflammatory gene upregulation, natural primary DENV-1 infection was accompanied with a more pronounced suppression in gene products associated with protein translation and mitochondrial function, principally in monocytes. This suggests that the immune response elicited by experimental and natural primary DENV infection are similar, but that natural primary DENV-1 infection has a more pronounced impact on basic cellular processes to induce a multi-layered anti-viral state.

Single-cell temporal analysis of natural dengue infection reveals skin-homing lymphocyte expansion one day before defervescence

“…At Day −2, the earliest time point in our study, we already observed the up-regulation of genes associated with type I interferon and response to virus in all major immune cell types ( Figure 2 C). This is in line with previous reports showing prominent expression of type I interferons at early phases of DENV infection ( Popper et al., 2012 ; Sun et al., 2013 ; van de Weg et al, 2015 ; Waickman et al., 2021 ), even though the exact timelines of the infection were characterized slightly differently in each study. In this study, we were able to pinpoint that the type I interferon pathway was most pronounced in monocytes.…”

“…These allowed us to improve the depth of earlier transcriptomic analyses of the host immune response against DENV, which might partly be restricted by the low-resolution bulk RNA-seq and microarray ( Hanley et al., 2021 ; Popper et al., 2012 ; Sun et al., 2013 ; van de Weg et al, 2015 ). Although most of the time-course RNA-seq studies of immune response in dengue patients or in vitro systems were performed using the samples collected during the vaguely defined “acute infection” or “febrile phase” ( Hanley et al., 2021 ; Sun et al., 2013 ; van de Weg et al, 2015 ; Waickman et al., 2021 ), we broke this important period down to three consecutive days, analyzed the single-cell transcriptomic profiles of DENV patients for each day, and compared those with the two-week follow-up baselines.…”

“…To overcome the limitations of the bulk high-throughput analyses, single-cell technology has recently been employed to dissect the responses of different immune cells to the DENV infection, e.g., ( Patil et al., 2018 ; Waickman et al., 2019 , 2021 ; Zanini et al., 2018 ). Using single-cell RNA-seq (scRNA-seq), Patil et al.…”

“…These studies showcased how single-cell technology provides in-depth insights into the immune responses to the DENV infection at unprecedented single cell levels, but all focused at particular time points or cell types during the course of infection. More recently, for the first time scRNA-seq has been implemented to investigate the transcriptomic patterns of experimental and natural primary DENV-1 infections at multiple time points ( Waickman et al., 2021 ). The study provided insights into common and specific patterns of immune response between the experimental and natural primary infections, however, it did not particularly focus on detailed transcriptional changes on the days leading to the clinically critical period of defervescence.…”

Artificial Neural Networks for classification of single cell gene expression

“…Peripheral blood mononuclear cells (PBMC) are circulating immune cells with a single round nucleus in the blood and are common diagnostic and prognostic targets [3]. PBMC are important targets of single-cell studies because they are indicators of immune status and are studied in cancer [4][5], infectious disease [6][7], and autoimmunity [8][9][10], among others. Five major cell types that constitute PBMC are B cells (BC), dendritic cells (DC), monocytes (MC), natural killer cells (NK), and T cells (TC) [11].…”