Theranostics 2022; 12(10):4606-4628. doi:10.7150/thno.72760 This issue

Research Paper

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

Ren-qi Yao1,2,3*, Zhi-xuan Li1*, Li-xue Wang1, Yu-xuan Li1, Li-yu Zheng1, Ning Dong1, Yao Wu1, Zhao-fan Xia2,3, Timothy R. Billiar4, Chao Ren1✉, Yong-ming Yao1✉

1. Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100853, China.
2. Department of Burn Surgery, the First Affiliated Hospital of Naval Medical University, Shanghai 200433, China.
3. Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Beijing 100730, China.
4. Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA.
* These authors contributed equally to this manuscript.

This is an open access article distributed under the terms of the Creative Commons Attribution License ( See for full terms and conditions.
Yao Rq, Li Zx, Wang Lx, Li Yx, Zheng Ly, Dong N, Wu Y, Xia Zf, Billiar TR, Ren C, Yao Ym. Single-cell transcriptome profiling of the immune space-time landscape reveals dendritic cell regulatory program in polymicrobial sepsis. Theranostics 2022; 12(10):4606-4628. doi:10.7150/thno.72760. Available from

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Graphic 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.

Keywords: single-cell analysis, sepsis, immunosuppression, dendritic cells