Dynamic LTR retrotransposon transcriptome landscape in septic shock patients

Abstract

Background: Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection. Numerous studies have explored the complex and dynamic transcriptome modulations observed in sepsis patients, but a large fraction of the transcriptome remains unexplored. This fraction could provide information to better understand sepsis pathophysiology. Multiple levels of interaction between human endogenous retroviruses (HERV) and the immune response have led us to hypothesize that sepsis is associated with HERV transcription and that HERVs may contribute to a signature among septic patients allowing stratification and personalized management.

Methods: We used a high-density microarray and RT-qPCR to evaluate the HERV and Mammalian Apparent Long Terminal Repeat retrotransposons (MaLR) transcriptome in a pilot study that included 20 selected septic shock patients, stratified on mHLA-DR expression, with samples collected on day 1 and day 3 after inclusion. We validated the results in an unselected, independent cohort that included 100 septic shock patients on day 3 after inclusion. We compared septic shock patients, according to their immune status, to describe the transcriptional HERV/MaLR and conventional gene expression. For differential expression analyses, moderated t tests were performed and Wilcoxon signed-rank tests were used to analyze RT-qPCR results.

Results: We showed that 6.9% of the HERV/MaLR repertoire was transcribed in the whole blood, and septic shock was associated with an early modulation of a few thousand of these loci, in comparison to healthy volunteers. We provided evidence that a subset of HERV/MaLR and conventional genes were differentially expressed in septic shock patients, according to their immune status, using monocyte HLA-DR (mHLA-DR) expression as a proxy. A group of 193 differentially expressed HERV/MaLR probesets, tested in an independent septic shock cohort, identified two groups of patients with different immune status and severity features.

Conclusion: We demonstrated that a large, unexplored part of our genome, which codes for HERV/MaLR, may be linked to the host immune response. The identified set of HERV/MaLR probesets should be evaluated on a large scale to assess the relevance of these loci in the stratification of septic shock patients. This may help to address the heterogeneity of these patients.

Keywords: HERV transcriptome; Immunosuppression; Septic shock patients; Whole blood; mHLA-DR expression.

Fig. 1

Schematic representation of the data process analysis. Healthy volunteers and both septic shock patient cohort subsets (IMMUNOSEPSIS and MIP-Rea) are defined on the left. Bioinformatics analysis parameters used for each step are described in the middle. Finally, the three phases of the data process analysis (descriptive phase, discovery phase, and validation phase) are presented. TP time point, D day

Fig. 2

HERV/MaLR transcriptome landscape in the whole blood (descriptive phase). a Percentages and absolute counts (number presented inside the bars) of expressed loci (probeset intensity above threshold), within individual groups of “HERV_prototypes,” “HERV_Dfam,” and “MaLR_Dfam” repertoires. “HERV_prototypes” were grouped by classes of retroviruses, namely gamma-retrovirus (green), beta-retrovirus (pink), and spuma-epsilon like retrovirus (blue). “HERV and MaLR Dfam” repertoires are depicted as a global homogeneous entity (purple). b Volcano plots derived from the HERV/MaLR differential expression analysis, between septic shock patients and HV on day 1 (left) or day 3 (right). The x-axis represents the log₂ fold change values and the y-axis represents the -log₁₀ adjusted P values. Each point represents a given probeset. Statistically and biologically significant probesets (adjusted P value < 0.05, │log₂FC│ > 1) are colored (red = downregulated, green = upregulated). c Venn diagrams from the HERV/MaLR differential expression analyses, according to the day of sampling and mHLA-DR expression (compared to HV). Upregulated probesets are in green and downregulated probesets are in red

Fig. 3

The differential expression of HERV/MaLR according to the immune status of septic shock patients (discovery phase). a Principal component analysis developed from the HERV expression matrix. Healthy volunteers, patients with normal expression of mHLA-DR, and patients with low expression of mHLA-DR are indicated in gray, pink, and blue, respectively. b Venn diagrams from HERV/MaLR differential expression analyses, according to the day of sampling and mHLA-DR expression (compared between septic shock patient groups). Upregulated probesets are in green and downregulated probesets are in red. c The table shows the number of statistically significant differentially expressed loci (DELs) for HERV/MaLR, differentially expressed genes (DEGs), and the corresponding number of probesets, respectively. Downregulated loci are in red, upregulated loci are in green. For HERV/MaLR loci, the name, number of differentially expressed probesets (between brackets), and chromosomal locations (in italic) are indicated (GRCh38 genome version) for the five most differentially expressed loci. For genes, the official gene symbol and the number of differentially expressed probesets (between brackets) are indicated