This study was carried out based on the hypothesis that “transcriptional profile heterogeneity will reflect patient clinical heterogeneity” and also identify gene signatures that may serve as biomarkers of staphylococcus infection in human”. It is our goal to identify the genes which exhibit differential expression in pneumonia infection induced by staphylococcus aureus. One of the most common uses of sequencing data is differential gene expression (DGE) analysis. This method is commonly utilized in many sequencing data analysis applications since it enables for the identification of differentially expressed genes across two or more conditions. Due to the variety of formats based on the tool of choice and the multiple bits of information contained in these results files, interpreting DGE findings can be difficult and time consuming (Wang et al., 2019). In the ICU, Staphylococcus aureus is the second most prevalent cause of pneumonia. Toxins and enzymes produced by the bacteria highlight its virulence, causing significant lung tissue damage. Clinical signs are insufficient to identify Staphylococcus aureus pneumonias from those caused by other pathogens, and clinical diagnosis suffers from the same limitations as other bacterial pneumonia causes (Hooper and Smith, 2012).
The comparison groups set for differential analysis in this study include staphylococcus aureus infected patients, staphylococcus infected patients with pneumonia infection and staphylococcus infected patients without pneumonia infection. The infection present aside pneumonia included bacteremia, osteomyelitis, suppurative arthritis, pyomyositis, empyema, abscess. Downregulation of gene expression is an indication of the inhibitory activity of the pathogen while the genes whose expression were upregulated are involved in the host defense against the pathogen (Shirahama et al., 2020). The downregulated genes during staphylococcus infection include KLRF1, P2RY10, CMKLR1, CD79A, GZMB, KLRF1, SH2D1B, FGFBP2, CXCL8, FCER1A. KLRK1 is a type II transmembrane-anchored glycoprotein that is expressed on the surface of Natural Killer (NK) cells, gamma/delta TcR + T cells, CD8 + T cells, and a modest subset of CD4 + T cells as a disulfide-linked homodimer. It binds to the DAP10 signaling protein non-covalently and sends activating or costimulatory signals to NK cells and T cells. NKG2D interacts to a family of glycoproteins called MICA, MICB, and ULBP1-6 membrane proteins in humans, which are commonly produced on cells that have been infected with pathogens or transformed. In comparison to adults, infants are more susceptible to many infections, which can be related to their undeveloped innate and adaptive immunity. Without pre-sensitization, natural killer cells provide first-line innate immune reactions against infected cells (Land, 2018). Lanier (2015), proved that the expression of KLRG1 on T cells improves during M. tuberculosis infection and declines after treatment, suggesting a correlation between KLRG1 expression and disease progression. The decrease in KLRG1 observed in this study may not be unconnected to the undeveloped immunity in pediatrics. The genes which contributed tremendously to the host defense against staphylococcus aureus infection include CAMP, LCN2, PGLYRP1, MYL9, ANKRD22, CETP, RNASE2, ASGR2, PLOD2. Cathelicidin antimicrobial peptide has the highest change in expression value. CAMP expression is also a member of the of the pneumonia infection associated/related genes (PIAGs) (Fig. 5).
Cathelicidin is an antibacterial peptide of the cathelicidin family. It is a small molecule (composed of 12–100 amino acids) with wide antibacterial activity that is thought to play a role in the innate immunity as the first line of defense against microbes. (Iacob and Iacob, 2014). When cathelicidin is produced enzymatically, it has an N-terminal prosequence followed by a C-terminal variable sequence with strong microbial activity. This antimicrobial peptide group is called cathelicidin because the structure of the prosequence is extremely similar to that of a protein called cathelin. Although the exact method of CAMP (Cathelicidin Antimicrobial Peptide) gene regulation is unknown, cathelicidin is reported to be upregulated when bacteria are present (Wang et al., 2021). Bacterial compounds have been found to boost Cathelicidin production in cultured human cells, showing that Cathelicidin plays a role in infection resistance. Several compounds, including 1,25-dihydroxyvitamin D3 (1,25(OH)2 D3), an active form of vitamin D, have been described as potent inducers of CAMP gene expression. Butyrate, Trichostatin A, Lithocholic acid, Interleukin-6, 1,25(OH)2 D3 (Pineda et al., 2019, Febriza et al., 2019). The physical structure of cathelicidin, as well as its cationic and hydrophobic characteristics, are responsible for the majority of its antimicrobial activities. The N-terminal helix is involved in chemotaxis and proteolisis defense, while the C-terminal helix is involved in antimicrobial activity. Cathelicidin binds to the surface of the microbial membrane, covers it, and perforates it, generating pores on the membrane that finally kill the bacteria. (Lv et al., 2014). Unlike zwitterionic eukariotic membranes, cathelicidin attaches to cell membranes that contain lipopolysaccharide (Gram-negative) or teichoic acid (Gram-positive) with a negative charge. With the contact between the capsule membrane and the protein capsid, cathelicidin also exhibits antiviral properties (Steinbuch and Fridman, 2016). Cathelicidin binds to the bacterial membrane in oligomeric forms, altering the subsequent contact and permeabilization manner. Because the monomeric peptide is less susceptible to sequestration by serum or medium components, as well as components of the bacterial outer cell wall, this has a significant impact on antibacterial action. In staphylococcus infection and tuberculosis, cathelicidin can bind to lipoteikoic acid and lipoarabinomannan, preventing macrophage activation. In some circumstances, resistant bacteria's protolithic enzymes can destroy cathelicidin and other antimicrobial peptides (Rowe-Magnus et al., 2019).
Among the pneumonia infection associated/related genes (PIAGs), Carcinoembryonic antigen related cell adhesion molecule 8 (CEACAM8) was highly upregulated and has interaction with Cathelicidin Antimicrobial Peptide (CAMP) which is also the highest upregulated among staphylococcus infection associated genes (SIAGs). The significant increase in the expression of CEACAM8 suggests the it may have a role in the interaction of staphylococcus aureus with neutrophils (Sarantis and Gray-Owen, (2012). CEACAM molecules are membrane glycoproteins that mediate intercellular interactions that influence cellular proliferation, immune cell activation, apoptosis, and tumor suppression. To establish a close interaction with host cells and tissues, a vast number of bacterial pathogens target cell adhesion molecules. Specific bacterial surface proteins typically identify members of the integrin, cadherin, and immunoglobulin-related cell adhesion molecule (IgCAM) families. Following cytoskeletal rearrangements triggered by receptor clustering, binding might cause bacterial internalization. Furthermore, signals from occupied receptors can cause cellular responses such as gene expression events, which affect the infected cell's phenotypic (Mix et al., 2021).