Using RNA-Seq to Investigate Immune-Metabolism Features in Immunocompromised Patients With Sepsis

Abstract

Objective: Sepsis is life threatening and leads to complex inflammation in patients with immunocompromised conditions, such as cancer, and receiving immunosuppressants for autoimmune diseases and organ transplant recipients. Increasing evidence has shown that RNA-Sequencing (RNA-Seq) can be used to define subendotype in patients with sepsis; therefore, we aim to use RNA-Seq to identify transcriptomic features among immunocompromised patients with sepsis. Methods: We enrolled patients who were admitted to medical intensive care units (ICUs) for sepsis at a tertiary referral centre in central Taiwan. Whole blood on day-1 and day-8 was obtained for RNA-Seq. We used Gene Set Enrichment Analysis (GSEA) to identify the enriched pathway of day-8/day-1 differentially expressed genes and MiXCR to determine the diversity of T cell repertoire. Results: A total of 18 immunocompromised subjects with sepsis and 18 sequential organ failure assessment (SOFA) score-matched immunocompetent control subjects were enrolled. The ventilator-day, ICU-stay, and hospital-day were similar between the two groups, whereas the hospital mortality was higher in immunocompromised patients than those in immunocompetent patients (50.0 vs. 5.6%, p < 0.01). We found that the top day-8/day-1 upregulated genes in the immunocompetent group were mainly innate immunity and inflammation relevant genes, namely, PRSS33, HDC, ALOX15, FCER1A, and OLR1, whereas a blunted day-8/day-1 dynamic transcriptome was found among immunocompromised patients with septic. Functional pathway analyses of day-8/day-1 differentially expressed genes identified the upregulated functional biogenesis and T cell-associated pathways in immunocompetent patients recovered from sepsis, whereas merely downregulated metabolism-associated pathways were found in immunocompromised patients with septic. Moreover, we used MiXCR to identify a higher diversity of T cell receptor (TCR) in immunocompetent patients both on day-1 and on day-8 than those in immunocompromised patients. Conclusions: Using RNA-Seq, we found compromised T cell function, altered metabolic signalling, and decreased T cell diversity among immunocompromised patients with septic, and more mechanistic studies are warranted to elucidate the underlying mechanism.

Keywords: RNA-Seq; immune; immunocompromised; metabolism; pathway analyses; sepsis.

Figure 1

Principal component analysis of day-1 transcriptome among all of the enrolled patients with septic (A) and volcano plots of differentially expressed genes between day-1 and day-8 in immunocompetent (B,D) and immunocompromised (C,E) patients with sepsis.

Figure 2

Network of enriched gene ontology term clusters in immunocompetent patients with sepsis. Red circles represent the upregulated pathways, and blue circles represent the downregulated pathways.

Figure 3

Network of enriched gene ontology term clusters in immunocompromised patients with sepsis. Blue circles represent the downregulated pathways.

Figure 4

Diversity of the T cell receptor. Counts (A), Shannon's diversity index (B), and inverse Simpson index (C) of unique CDR3. (CDR3, complementarity-determining region-3). * < 0.05, ** < 0.005.