The present study is the first study to conduct a comprehensive bioinformatics analysis to explore hub genes and biological pathways related to LPS and HMGB1 triggered sepsis-associated ALI. The present study identified 534 and 317 DEGs for LPS- and HMGB1-induced ALI, respectively. The biological pathways involved in LPS- and HMGB1-induced ALI were also demonstrated accordingly. By conducting PPI network analysis, we found that ten hub genes for LPS-induced ALI (CXCL8, TNF, IL6, IL1B, ICAM1, CXCL1, CXCL2, IL1A, IL1RN and CXCL3) and another ten hub genes for HMGB1-induced ALI (CCL20, CXCL2, CXCL1, CCL4, CXCL3, CXCL9, CCL21, CXCR6, KNG1 and SST). Notably, by combining analysis, the results revealed a module of genes TNF, CCL20, IL1B, NFKBIA, CCL4, PTGS2, TNFAIP3, CXCL2, CXCL1 and CXCL3 were potential biomarkers for sepsis-associated ALI.
To further explore the mechanisms of LPS-triggered sepsis-associated ALI, we searched the literatures for the functions of LPS relevant 10 genes (CXCL8, TNF, IL6, IL1B, ICAM1, CXCL1, CXCL2, IL1A, IL1RN and CXCL3). The functions of these ten genes were summarized in Table 2. The cellular components encoded by these 10 genes were all previously proved to be participated in the progression of inflammations in sepsis patients or animal models [15–24]. For chemokine ligand family, CXCL1, CXCL2, CXCL3 and CXCL8, the common functions are all chemoattractant for neutrophils [15, 20–21, 24]. And for interleukin family, IL1A, IL1B, ILRN and IL6, their common functions are rapid increasing in levels and evoking “cytokine storm” [17–18, 22–23]. For ICAM1, stimulated by LPS, resulted in increases in neutrophil-neutrophil adherence and aggregation [19]. And for TNF, the most common mediator of sepsis, elicit the release of inflammatory mediators [16]. LPS may stimulate these cellular components to aggravate the progression of sepsis-induced lung injury.
Table 2
Hub genes and their functions in inflammation of sepsis based on previous literatures (for LPS-induced ALI)
Hub genes | Cellular components | Reference | Functions mentioned in the literatures |
CXCL8 | Chemokine (C-X-C motif) ligand 8 | T M Cunha et al [15] | Recruiting leukocytes from the blood into tissues during inflammation |
TNF | Tumor necrosis factor | Lucy K Reiss et al [16] | Eliciting the release of inflammatory mediators, and mediator of sepsis itself |
IL6 | Interleukin 6 | Tanaka T et al [17] | Excessive synthesis of IL-6 while fighting environmental stress leads to an acute severe systemic inflammatory response known as 'cytokine storm' |
IL1B | Interleukin-1-B | Varljen T et al [18] | Proinflammatory mediator whose level is rapidly increased during infection |
ICAM1 | Intercellular-adhesion-molecule-1 | Ode Y et al [19] | An increased expression of ICAM-1 on neutrophils after stimulation with LPS has been shown, which resulted in significant increases in neutrophil-neutrophil adherence and aggregation |
CXCL1 | Chemokine (C-X-C motif) ligand 1 | Paudel S et al [20] | CXCL1 induces neutrophil influx during bacterial infections, in addition, it is a central player in host defense, granulopoiesis, and mobilization of neutrophils during sepsis. |
CXCL2 | Chemokine (C-X-C motif) ligand 2 | De Filippo et al [21] | CXCL2 is secreted, especially by mast cells, monocytes, and macrophages at the site of inflammation, and is an important chemotactic for neutrophils during infections |
IL1A | Interleukin-1-A | Zhu W et al [22] | IL-1 signaling via the type 1 IL-1 receptor leads to multiple inflammatory effects including vasodilation, increased vascular permeability |
IL1RN | Interleukin-1-RN | Meyer et al [23] | C allele of a synonymous coding variant (rs315952-C) in IL1RN is associated with reduced risk for ARDS and increased plasma IL-1ra |
CXCL3 | Chemokine (C-X-C motif) ligand 3 | Rebollo J [24] | CXCL3 has been shown to act as a chemoattractant for neutrophils to and for cerebellar progenitor cells |
Besides, we also searched previous literatures and screened for the studies with the ten hub genes for HMGB1 triggered ALI. The cellular components encoded by these 10 genes were all previously proved to be participated in the progression of inflammations in sepsis patients or animal models. [20–21, 24, 25–31] For chemokine ligand family, CXCL1, CXCL2, CXCL3 and CXCL9, the common functions are all chemoattractant for neutrophils. [25, 28–29] For CC chemokine family, CCL4 plays key roles in chemotaxis as well as enhancement of the inflammatory response, while CCL21 regulates leukocyte trafficking and homing to the lymph nodes. [26, 28] In addition, CCL20 is an early trigger of neutrophil cell recruitment and activation of T cells in the small intestine. [27] For CXCR6, it could mediate iNKT-cell accumulation, clustering and arrest within the liver in several inflammatory conditions. [29] For KNG1, it could accelerate the progress of cellular inflammation. [30] Besides, SST has a protective effect on intestinal barrier dysfunction through the suppression of NF-κB. [31] HMGB1 may stimulate all these cellular biomarkers to aggravate the progression of sepsis-induced lung injury. These functions of ten hub genes for HMGB1-induced ALI were listed in Table 3.
Table 3
Hub genes and their functions in inflammation of sepsis based on previous literatures (for HMGB1-induced ALI)
Hub genes | Cellular components | Reference | Functions mentioned in the literatures |
CXCL9 | Chemokine (C-X-C motif) ligand 9 | Cavalcanti et al [15] | CXCL9 induces the CXC chemokines which act preferentially on T and B lymphocytes and natural killer cells (NK) |
CCL4 | Chemokine (C-C motif) ligand 4 | Nowak et al [16] | CCL4 is a member of the CC chemokine family, and is produced by numerous cell types including monocytes, neutrophils, T and B lymphocytes, NK cells, and dendritic cells. It plays a key role in chemotaxis as well as enhancement of the inflammatory response |
CCL20 | Chemokine (C-C motif) ligand 20 | Kitagawa Y et al [17] | CCL20 has been identified as an early trigger of neutrophil cell recruitment and activation of T cells in the small intestine. |
CCL21 | Chemokine (C-C motif) ligand 21 | Castro R et al [18] | The regulation of leukocyte trafficking and homing to the lymph nodes (LNs) |
CXCR6 | Chemokine (C-X-C motif) receptor 6 | Young et al [19] | CXCR6 has been shown to mediate iNKT-cell accumulation, clustering and arrest within the liver in several inflammatory conditions |
CXCL1 | Chemokine (C-X-C motif) ligand 1 | Paudel S et al [20] | CXCL1 induces neutrophil influx during bacterial infections, in addition, it is a central player in host defense, granulopoiesis, and mobilization of neutrophils during sepsis. |
CXCL2 | Chemokine (C-X-C motif) ligand 2 | De Filippo et al [21] | CXCL2 is secreted, especially by mast cells, monocytes, and macrophages at the site of inflammation, and is an important chemotactic for neutrophils during infections |
KNG1 | Kininogen-1 | Hu Q et al [22] | As a pro-inflammatory cytokine, KNG1 has been demonstrated to accelerate the progress of inflammation. Inhibition of KNG1 could relieve cellular inflammation |
SST | Somatostatin | Xu X [23] | SST has a protective effect on intestinal barrier dysfunction through the suppression of NF-κB |
CXCL3 | Chemokine (C-X-C motif) ligand 3 | Rebollo J [24] | CXCL3 has been shown to act as a chemoattractant for neutrophils to and for cerebellar progenitor cells |
Finally, we searched previous publications and screened for studies with the ten potential key genes for sepsis-associated ALI. As we descripted previously, TNF, CCL20, IL1B, CCL4, CXCL2, CXCL1, CXCL3 were listed in Table 2 and Table 3. However, NFKB1A, PTGS2 and TNFAIP3 were newly recognized in the combining analysis, as shown in Table 4.
Table 4
Hub genes and their functions in inflammation of sepsis based on previous literatures (for sepsis-associated ALI)
Hub genes | Reference | Functions mentioned in the literatures |
NFKB1A | Yenmis et al [32] | NFKB1A have a genetic effect on the development of a variety of inflammatory diseases associated with altered immune response |
PTGS2 | Li N et al [16] | LPS increased the levels of ferroptotic markers involving prostaglandin endoperoxide synthase 2 (PTGS2) |
CCL20 | Jae-Min Yuk et al [17] | Toll-like receptor (TLR)-induced inflammation could be promoted by Tnfaip3 transcription and fine-tuning of metabolic reprogramming in macrophages |
In spite that we identified several novel genes that may involve in the progression of sepsis-associated ALI, there are still several limitations in this study. Firstly, lack of experimental verification is the main drawback of this study. Further explorable studies in vivo or in animals should be conducted to investigate the weighted value of these hub genes. Secondly, due to limited sample size of neutrophils of sepsis patients, we failed to conduct a survival analysis based on these data. Nevertheless, our study still provided substantial implications for diagnosing and treating sepsis-induced ALI.