Single-cell transcriptome profiling of the immune space-time landscape reveals dendritic cell regulatory program in polymicrobial sepsis

Abstract

Rationale: Evident immunosuppression has been commonly seen among septic patients, and it is demonstrated to be a major driver of morbidity. Nevertheless, a comprehensive view of the host immune response to sepsis is lacking as the majority of studies on immunosuppression have focused on a specific type of immune cells. Methods: We applied multi-compartment, single-cell RNA sequencing (scRNA-seq) to dissect heterogeneity within immune cell subsets during sepsis progression on cecal ligation and puncture (CLP) mouse model. Flow cytometry and multiplex immunofluorescence tissue staining were adopted to identify the presence of 'mature DCs enriched in immunoregulatory molecules' (mregDC) upon septic challenge. To explore the function of mregDC, sorted mregDC were co-cultured with naïve CD4 + T cells. Intracellular signaling pathways that drove mregDC program were determined by integrating scRNA-seq and bulk-seq data, combined with inhibitory experiments. Results: ScRNA-seq analysis revealed that sepsis induction was associated with substantial alterations and heterogeneity of canonical immune cell types, including T, B, natural killer (NK), and myeloid cells, across three immune-relevant tissue sites. We found a unique subcluster of conventional dendritic cells (cDCs) that was characterized by specific expression of maturation- and migration-related genes, along with upregulation of immunoregulatory molecules, corresponding to the previously described 'mregDCs' in cancer. Flow cytometry and in stiu immunofluorescence staining confirmed the presence of sepsis-induced mregDC at protein level. Functional experiments showed that sepsis-induced mregDCs potently activated naive CD4 + T cells, while promoted CD4 + T cell conversion to regulatory T cells. Further observations indicated that the mregDC program was initiated via TNFRSF-NF-κB- and IFNGR2-JAK-STAT3-dependent pathways within 24 h of septic challenge. Additionally, we confirmed the detection of mregDC in human sepsis using publicly available data from a recently published single-cell study of COVID-19 patients. Conclusions: Our study generates a comprehensive single-cell immune landscape for polymicrobial sepsis, in which we identify the significant alterations and heterogeneity in immune cell subsets that take place during sepsis. Moreover, we find a conserved and potentially targetable immunoregulatory program within DCs that associates with hyperinflammation and organ dysfunction early following sepsis induction.

PINK1 protects against dendritic cell dysfunction during sepsis through the regulation of mitochondrial quality control

“…The changes in DC function may contribute to immunosuppression and mortality during sepsis (Yao et al 2022 ). To verify this process, we first examined the changes in DC function during sepsis in vivo.…”

Mature dendritic cells enriched in immunoregulatory molecules (mregDCs): A novel population in the tumour microenvironment and immunotherapy target

“… 48 The mregDC program can also be driven by sepsis and is tightly associated with hyperinflammatory stages. 49 To identify differences in mregDCs in the tumour versus inflammatory condition, Mair et al. 28 compared the single‐cell transcriptome of mregDCs in inflamed tissue of the oral mucosa and in oral squamous carcinoma.…”

“…Therefore, modulation of mregDC function and cytokine secretion with targeted drugs might contribute to alleviate the AD and PSO 48 . The mregDC program can also be driven by sepsis and is tightly associated with hyperinflammatory stages 49 . To identify differences in mregDCs in the tumour versus inflammatory condition, Mair et al 28 .…”

Expert consensus on the monitoring and treatment of sepsis-induced immunosuppression

“…11 Department of Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, China. 12 Department of Critical Care Medicine, General Hospital of Eastern Theater Command of Chinese PLA, Nanjing 210002, China. 13 Department of Surgical Intensive Critical Unit, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China.…”

“…Although lymphocyte count is easily obtained, its specificity is relatively low due to many confounding factors; meanwhile, mHLA-DR detection requires complex equipment with high detection cost, and the definition of early warning threshold remains inconclusive [9]. In recent years, investigators have applied multi-omic approaches to explore immune monitoring, aiming to discover new sepsis-related cell subsets and biomarkers, yet their translational significance and value need to be further validated by large-scale clinical trials [10][11][12]. Meanwhile, researchers are still debating on patient selection, treatment timing, dosage, drug combination, treatment duration, indications for discontinuation, and efficacy evaluation for immunomodulatory therapy in patients with sepsis that has not been evaluated in large-scale, high-quality clinical randomized controlled trials (RCTs) [13][14][15].…”