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Integrated analysis reveals NLRC4 as a potential biomarker in sepsis pathogenesis

Genes & Immunity (2024)Cite this article

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Abstract

Sepsis remains a significant global health burden and contributor to mortality, yet the precise molecular mechanisms underlying the immune response are not fully elucidated. To gain insight into this issue, we performed a comprehensive analysis using a variety of techniques including bulk RNA sequencing, single-cell RNA sequencing, and enzyme-linked immunosorbent assay (ELISA). We performed enrichment analysis of differentially expressed genes in sepsis and healthy individuals by utilizing Gene Ontology (GO) analysis and indicated significant enrichment of immune-related response. Following Weighted Gene Co-Expression Network Analysis (WGCNA) and protein-protein interaction analysis (PPI) were used to identify key immune-related hub genes and validated by ELISA to show that NLRC4 is highly expressed in sepsis. Additionally, an analysis of scRNA-seq data from newly diagnosed sepsis, sepsis diagnosis at 6 hours, and healthy samples demonstrates a significant increase in both the expression levels and proportions of NLRC4 in sepsis monocytes and neutrophils. In addition, using pySCENIC we identified upstream transcription factors that regulate NLRC4. Our study provides valuable insights into the identification of NLRC4 in peripheral blood as a potential candidate gene for the diagnosis and treatment of sepsis.

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Fig. 1
Fig. 2: Identification of differentially expressed genes (DEGs) between Sepsis, healthy, and noninfectious samples from the GSE134347 dataset.
Fig. 3: Identification of key immune-related central genes associated with sepsis using WGCNA and PPI networks.
Fig. 4: Verification of expression levels of MAP2K6 and NLRC4.
Fig. 5: Analysis of scRNA-seq and CIBERSORT.
Fig. 6: Based on the pySCENIC algorithm, upstream transcription factor features of key genes were obtained.

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Data availability

No new data were created in this study and all data in the articles are annotated. All data (GSE134347, GSE65682, GSE28750, and GSE167363) and study design details in this study for the GEO can be found online at https://www.ncbi.nlm.nih.gov/geo/.

Code availability

Code available on request from corresponding author.

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Acknowledgements

The authors gratefully acknowledge all participants and staff for their contribution to the study. The authors thank all members of the GZDlab for participating in the discussion of this artical with the first author and for their help and support.

Funding

This work is funded by China National Natural Youth Science Foundation (81802078), Zhejiang Provincial Department of Science and Technology “Leading Geese” research and development projects (2023C03083) and Zhejiang Province Public Welfare Technology Application Research Project (GF20H200021).

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Author notes

  1. These authors contributed equally: Yinghe Xu, Hui Zhao, Jiaxi Chen.

Authors and Affiliations

  1. School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310013, China

    Chunhui Jiang, Jiani Chen & Jiaxi Chen

  2. Taizhou Hospital of Zhejiang, Wenzhou Medical University, Linhai, 318000, China

    Chunhui Jiang, Jiani Chen, Jiaqing Xu, Chen Chen, Hongguo Zhu, Yinghe Xu, Hui Zhao & Jiaxi Chen

  3. Department of Laboratory Medicine, Enze Hospital, Taizhou Enze Medical Center (Group), Taizhou, 318000, China

    Chunhui Jiang, Jiani Chen, Jiaqing Xu, Chen Chen, Hongguo Zhu, Yinghe Xu, Hui Zhao & Jiaxi Chen

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Contributions

Yinghe XU, Hongguo Zhu, and Jiaxi Chen were involved in the conception and design. Chunhui Jiang and Jiani Chen. were involved in the analysis and interpretation of the data. Jiaqing Xu, Hui Zhao, Chen Chen, and Hongguo Zhu. critically revised it for intellectual content. Chunhui Jiang, Jiani Chen, and Jiani Chen participated in drafting the manuscript. All authors agree to be accountable for all aspects of the work.

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Correspondence to Yinghe Xu, Hui Zhao or Jiaxi Chen.

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The authors declare no competing interests.

Ethics approval

The Ethics approval and consent to participate in the current study were obtained from the ethics committee of Taizhou Hospital of Zhejiang Province, affiliated with Wenzhou Medical University (Date: March 21, 2023/No.: K20230315), in accordance with the World Medical Association Declaration of Helsinki.

Informed consent

The data and specimens used in this study were obtained from previously collected clinical diagnostic and disease monitoring data, as well as residual samples from past patients, which were subsequently subjected to further experimental testing. The privacy and personal identity information of the subjects are protected, and there is no need for follow-up or additional information gathering from the participants. Therefore, an exemption from written informed consent was granted by the Taizhou Enze Medical Center (Group) Enze Hospital.

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Jiang, C., Chen, J., Xu, J. et al. Integrated analysis reveals NLRC4 as a potential biomarker in sepsis pathogenesis. Genes Immun (2024). https://doi.org/10.1038/s41435-024-00293-4

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