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Identification and evaluation of hub mRNAs and long non-coding RNAs in neutrophils during sepsis

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Abstract

Objective

To reveal the systematic response of neutrophils to sepsis and to study the hub lncRNAs in sepsis.

Materials and methods

Neutrophils taken from the femur and tibia of male C57 BL/6 mice were used in this study. And neutrophils were treated for 0 h, 0.5 h, 1 h, and 4 h with or without 1 µg/mL lipopolysaccharide (LPS) for further chip detection. In addition, cecal ligation and perforation were used to simulate sepsis. Here, we used different bioinformatics analyses, including differential expression analysis, weighted gene co-expression network analysis (WGCNA), and gene regulatory network analysis, to analyze the systemic response of neutrophils to sepsis.

Results

We identified nine modules and found hub lncRNAs in each module. The blue and pink modules were closely related to the inflammatory state of sepsis. Some hub lncRNAs (NONMMUT005259, KnowTID_00004196, and NR_003507) may have functions related to the inflammatory state in sepsis.

Conclusions

Based on a new biological approach, our research results revealed the systemic-level response of neutrophils to sepsis and identified several hub lncRNAs with potential regulatory effects on this condition.

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Acknowledgements

This study was supported by the National Natural Science Foundation of China, Nos. 81471903, and 81772135; by the Jiangsu Natural Science Foundation, No. BE2017695.

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Authors and Affiliations

  1. School of Medicine, Jiangsu University, Zhenjiang, 212001, Jiangsu Province, China

    Jiamin Huang & Ran Sun

  2. Department of Burns and Plastic Surgery, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215002, Jiangsu Province, China

    Bingwei Sun

Authors
  1. Jiamin Huang
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  2. Ran Sun
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  3. Bingwei Sun
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Correspondence to Bingwei Sun.

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11_2020_1323_MOESM1_ESM.tif

Supplementary file1 (TIF 983 kb) Weighted co-expression gene network analysis. (a) Sample cluster analysis. (b) Number of mRNAs and lncRNAs in each module. (c) Eigengene adjacency heatmap. Colors represent correlation between two modules: blue, low correlation; red, high correlation

11_2020_1323_MOESM2_ESM.tif

Supplementary file2 (TIF 1179 kb) GO enrichment of DEGs in the turquoise (a), green (b), and brown (c) modules. KEGG annotation of gene clusters in the turquoise (d), green (e), and brown (f) modules. Colors represent term enrichment: purple, low enrichment; red, high enrichment

11_2020_1323_MOESM3_ESM.tif

Supplementary file3 (TIF 2609 kb) Module lncRNA-mRNA-Net of hub genes in the turquoise (a), green (b), and brown (c) modules. Module lncRNA-mRNA-Pathway-Net of hub genes in the turquoise (d), green (e), and brown (f) modules. Green circles represent mRNAs, red triangles represent lncRNAs, and gray polygons represent pathways. The size of these graphs represents the level of intramodular connectivity of hub genes in the network

Supplementary file4 (DOCX 12 kb) Primer sequences of selected hub mRNAs and lncRNAs

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Huang, J., Sun, R. & Sun, B. Identification and evaluation of hub mRNAs and long non-coding RNAs in neutrophils during sepsis. Inflamm. Res. 69, 321–330 (2020). https://doi.org/10.1007/s00011-020-01323-3

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  • DOI: https://doi.org/10.1007/s00011-020-01323-3

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