Cell landscape of immunosuppressive reprogramming during fatal sepsis and severe-COVID-19 through scRNA-SEQ

Abstract

It is evident that some patients with sepsis and septic shock are admitted to hospitals late in their illness, contributing to poor outcomes and high mortality rates across all age groups worldwide. Current diagnostic and monitoring procedures often rely on delayed and inaccurate clinical identification, leading to suboptimal treatment decisions. Following the initial "cytokine storm", sepsis is frequently associated with immune system paralysis, highlighting the need for precise immunological subtyping for therapy. In sepsis, the immune system is activated to produce interleukins, and endothelial cells express increased levels of adhesion molecules. These processes lead to changes in circulating immune cell proportions, including a decrease in regulatory cells and an increase in memory and cytotoxic T cells. These alterations have lasting effects on CD8 T cell phenotype, mHLA-DR expression, and microRNA dysregulation. Aim: To investigate the pathophysiology of sepsis (bacterial and viral) and the immunosuppressive reprogramming of immune cells using an integrated immunological and -omics model approach. Methods: Peripheral blood mononuclear cells (PBMCs) were isolated using the Sepmate procedure. Single-cell 3 cDNA libraries were generated using the BD Rhapsody protocol. Our cohort from St. James's Hospital included 16 participants, encompassing both mild and severe cases of viral and bacterial sepsis. Libraries were sequenced with 150 bp paired-end reads on the Illumina HiSeq platform, achieving an average of 180 million reads per sample. Subsequent analyses included publicly available datasets to assess PBMC reprogramming in sepsis and COVID-19 compared to healthy donors, controlling for batch effects and the single-center study design. Findings: Critically ill COVID-19 patients exhibited a distinct immunosuppressive endotype, leading to inflammatory dysregulation even in moderate disease forms. Significant differences in CD8 naive T cells, CD4 naive T cells, and CD4 memory T cells were observed between COVID-19 and mild bacterial sepsis. However, severe infections (critical COVID-19 and bacterial septic shock) displayed shared immune patterns, including upregulated transcriptome profiles in B cells, classical monocytes, CD4 and CD8 naive T cells, and natural killer cells. Genes associated with myeloid-derived suppressor cell (MDSC) proliferative and immunosuppressive functions, such as CYBB/NOX2, S100A8/9, and RETN, were enriched in sepsis datasets. Transcriptomic similarities between the sepsis cohort and healthy controls were more pronounced at post-sepsis day 21, compared to those in septic shock. Cell cycle signature analysis from an in-silico atlas (11 datasets) highlighted the predominance of blood leukocytes (B, T, and NK cells) in COVID-19 severity and disease trajectory. Conclusion: Significant gene expression differences were identified based on infection etiology in mild cases (COVID-19 or bacterial sepsis). However, severe infections (critical COVID-19 and bacterial septic shock) shared immune profiles related to both adaptive and innate responses, irrespective of the cause. These findings may support the implementation of co-adjuvant therapies and interventions aimed at preventing the severe disease forms associated with high global mortality rates.