A Novel Single Cell RNA-seq Analysis of Non-Myeloid Circulating Cells in Late Sepsis

Front Immunol. 2021 Aug 16:12:696536. doi: 10.3389/fimmu.2021.696536. eCollection 2021.

Abstract

Background: With the successful implementation of the Surviving Sepsis Campaign guidelines, post-sepsis in-hospital mortality to sepsis continues to decrease. Those who acutely survive surgical sepsis will either rapidly recover or develop a chronic critical illness (CCI). CCI is associated with adverse long-term outcomes and 1-year mortality. Although the pathobiology of CCI remains undefined, emerging evidence suggests a post-sepsis state of pathologic myeloid activation, inducing suboptimal lymphopoiesis and erythropoiesis, as well as downstream leukocyte dysfunction. Our goal was to use single-cell RNA sequencing (scRNA-seq) to perform a detailed transcriptomic analysis of lymphoid-derived leukocytes to better understand the pathology of late sepsis.

Methods: A mixture of whole blood myeloid-enriched and Ficoll-enriched peripheral blood mononuclear cells from four late septic patients (post-sepsis day 14-21) and five healthy subjects underwent Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq).

Results: We identified unique transcriptomic patterns for multiple circulating immune cell subtypes, including B- and CD4+, CD8+, activated CD4+ and activated CD8+ T-lymphocytes, as well as natural killer (NK), NKT, and plasmacytoid dendritic cells in late sepsis patients. Analysis demonstrated that the circulating lymphoid cells maintained a transcriptome reflecting immunosuppression and low-grade inflammation. We also identified transcriptomic differences between patients with bacterial versus fungal sepsis, such as greater expression of cytotoxic genes among CD8+ T-lymphocytes in late bacterial sepsis.

Conclusion: Circulating non-myeloid cells display a unique transcriptomic pattern late after sepsis. Non-myeloid leukocytes in particular reveal a host endotype of inflammation, immunosuppression, and dysfunction, suggesting a role for precision medicine-guided immunomodulatory therapy.

Keywords: chronic critical illness; immune cells; lymphocytes; scRNA-seq; sepsis; transcriptome.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Bacterial Infections / blood
  • Bacterial Infections / genetics*
  • Bacterial Infections / immunology
  • Bacterial Infections / microbiology
  • Case-Control Studies
  • Dendritic Cells / immunology
  • Dendritic Cells / metabolism*
  • Dendritic Cells / microbiology
  • Female
  • Gene Expression Profiling*
  • Humans
  • Lymphocytes / immunology
  • Lymphocytes / metabolism*
  • Lymphocytes / microbiology
  • Male
  • Middle Aged
  • Mycoses / blood
  • Mycoses / genetics*
  • Mycoses / immunology
  • Mycoses / microbiology
  • Phenotype
  • RNA-Seq*
  • Sepsis / blood
  • Sepsis / genetics*
  • Sepsis / immunology
  • Sepsis / microbiology
  • Single-Cell Analysis*
  • Time Factors
  • Transcriptome*