Research Paper Volume 12, Issue 18 pp 18716—18740

Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets

Kaimin Mao1, *, , Wei Geng1, *, , Yuhan Liao1, *, , Ping Luo2, , Hua Zhong3, , Pei Ma1, , Juanjuan Xu1, , Shuai Zhang1, , Qi Tan1, , Yang Jin1, ,

  • 1 Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
  • 2 Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China
  • 3 College of Life Sciences, Wuhan University, Hubei Province, Wuhan, 430072, China
* Equal contribution

Received: May 2, 2020       Accepted: August 19, 2020       Published: September 23, 2020
How to Cite

Copyright: © 2020 Mao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are life-threatening clinical conditions predominantly arising from uncontrolled inflammatory reactions. It has been found that the administration of astaxanthin (AST) can exert protective effects against lipopolysaccharide (LPS)-induced ALI; however, the robust genetic signatures underlying LPS induction and AST treatment remain obscure. Here we performed a statistical meta-analysis of five publicly available gene expression datasets from LPS-induced ALI mouse models, conducted RNA-sequencing (RNA-seq) to screen differentially expressed genes (DEGs) in response to LPS administration and AST treatment, and integrative analysis to determine robust genetic signatures associated with LPS-induced ALI onset and AST administration. Both the meta-analyses and our experimental data identified a total of 198 DEGs in response to LPS administration, and 11 core DEGs (Timp1, Ly6i, Cxcl13, Irf7, Cxcl5, Ccl7, Isg15, Saa3, Saa1, Tgtp1, and Gbp11) were identified to be associated with AST therapeutic effects. Further, the 11 core DEGs were verified by quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC), and functional enrichment analysis revealed that these genes are primarily associated with neutrophils and chemokines. Collectively, these findings unearthed the robust genetic signatures underlying LPS administration and the molecular targets of AST for ameliorating ALI/ARDS which provide directions for further research.


ARDS: acute respiratory distress syndrome; ALI: acute lung injury; LPS: lipopolysaccharide; ROS: reactive oxygen species; TXNIP: thioredoxin interacting protein; Trx: thioredoxin; NLRP3: nucleotide-binding domain-like receptor protein 3; IL-1β: interleukin-1β; TNF-α: tumor necrosis factor-α; iNOS: inducible nitric oxide synthase; COX2: cyclooxygenase-2; AST: astaxanthin; NF-κB: nuclear factor kappaB; NO: nitric oxide; PGE2: prostaglandin E2; NOS: nitric oxide synthase; Drp1: dynamin-related protein-1; GEO: gene expression omnibus; VSN: variance stabilizing normalization; FDR: false discovery rate; DEGs: differentially expressed genes; dscDNA: double-stranded cDNA; PCR: polymerase chain reaction; PE: paired-end; GO: gene ontology; BP: biological process; MF: molecular function; CC: cell component; RT-PCR: reverse transcription-polymerase chain reaction; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; qRT-PCR: quantitative real-time polymerase chain reaction; IHC: immunohistochemistry; ANOVA: analysis of variance; RNA-seq: RNA-sequencing; IPF: idiopathic pulmonary fibrosis; ZBP1: Z-DNA binding protein 1; SAA: serum amyloid A; COVID19: corona virus disease 19; MALAT1: metastasis associated lung adenocarcinoma transcript 1; IRF7: interferon regulatory factor 7; IAV: influenza A virus; TRAF6: TNF receptor associated factor 6; TIMP1: tissue inhibitor of metalloproteinase-1; MMPs: matrix metalloproteinases; HSCs: hepatic stellate cells; ISG15: interferon-stimulated gene 15; IFIT: interferon induced protein with tetratricopeptide repeats.