Journal: Shock (Augusta, Ga.)

Article Title: A TRANSCRIPTOMIC APPRECIATION OF CHILDHOOD MENINGOCOCCAL AND POLYMICROBIAL SEPSIS FROM A PRO-INFLAMMATORY AND TRAJECTORIAL PERSPECTIVE, A ROLE FOR VASCULAR ENDOTHELIAL GROWTH FACTOR A AND B MODULATION?

doi: 10.1097/SHK.0000000000002192

Figure Lengend Snippet: Transcriptional changes in postmortem samples in Neisseria meningococcal sepsis versus controls . This figure represents an analysis of the postmortem dataset GSE141864, comparing individuals with noninfectious causes for death (controls) and patients diagnosed with Neisseria meningococcal septic shock (MSS). The data in A was organized based on gene symbol, and box plot analysis was conducted. In MSS cases, there was a significant upregulation of NFKB1 and VEGF-A GE compared with controls, whereas VEGF-B was downregulated. However, there was no difference in TNF GE between cases and controls. GE was used to analyze tissue from patients with MSS (B). TNF GE showed the highest upregulation in the heart compared with the kidneys and spleen, with no difference compared with the lungs. No significant differential GE was noted for NFKB1 across tissue types. In the kidneys, VEGF-A exhibited upregulation compared with the heart, lungs, and spleen, whereas VEGF-B showed upregulation in the heart compared with the lungs. A two-group comparison was performed between heart tissue and all other tissues using QOE ( P = 0.01 and q = 0.05). This analysis filtered 26,193 variables to 6,179 genes and generated a three-axis principal component analysis plot (C). The resulting differential gene set was then analyzed using the ShinyGo platform generating lollipop and tree plots (D and E). The ShinyGO platform was set for Homo sapiens and an FDR cutoff of 0.05 to display the top 30 pathways. The lollipop and tree plots depicted various aspects of the respiratory chain, aerobic respiration, and mitochondrial function pathways. A network plot was also generated from the gene 6,179 list, revealing networks associated with the heart muscle (F). A subset of 19 genes was removed from the gene list to comply with the Enrichr platform, resulting in 6,160 enriched genes showing enrichment by hexagon plots (G). Highly significant pathways included VEGF-A/VEGF-R, MAPK, P13k-Akt, IL-18, and focal adhesion. FDR, false discovery rate; GE, gene expression; NFKB1, NF-κB1; QOE, Qlucore Omics Explorer; VEGF, vascular endothelial growth factor; VEGF, VEGF receptor.

Article Snippet: Qlucore Omics Explorer (QOE) version 3.1 software (Qlucore AB, Lund, Sweden) was used to analyze the differential expression of genes.

Techniques: Comparison, Generated, Expressing

Journal: Shock (Augusta, Ga.)

Article Title: A TRANSCRIPTOMIC APPRECIATION OF CHILDHOOD MENINGOCOCCAL AND POLYMICROBIAL SEPSIS FROM A PRO-INFLAMMATORY AND TRAJECTORIAL PERSPECTIVE, A ROLE FOR VASCULAR ENDOTHELIAL GROWTH FACTOR A AND B MODULATION?

doi: 10.1097/SHK.0000000000002192

Figure Lengend Snippet: Transcript (cross-sectional) of the Wright dataset . The GSE80496 Neisseria meningococcal dataset was classified into healthy (controls, n = 21) and meningococcal disease (sepsis only, n = 21; sepsis with meningitis, n = 3) groups. Box plot analysis (A) showed elevated GE in patients with sepsis alone compared with both controls and patients with sepsis and meningitis. Specifically, NFKB1 and VEGF-A GE are elevated in patients with sepsis only, compared with controls, whereas VEGF-B GE is downregulated. GSE80496 dataset contains 18,631 variables when averaged according to gene symbol. Principal component analysis plot is illustrated (B). This dataset is then filtered in QOE ( P = 0.001 and q = 0.003), leading to 5,596 unique genes, which are then parsed through the ShinyGO platform (setting = Homo sapiens , FDR cutoff = 0.05, top pathways shown =30, database used = GO biological process). This results in the tree diagram (C) and lollipop plot shown (D). Also, the same gene list is pasted into the Enrichr tool, generating enriched pathways in the KEGG 2021 database category. These data are sent through an Appyter connection to generate a hexagon plot (E). The hexagonal canvas plot shows terms from the WikiPathway 2021 Human gene set library. Each hexagon in the plot represents a single term. The brighter the color, the higher the Jacquard similarity between the term gene set and the input gene set. Terms highlighted in blue show the most significant overlap with the input query gene set, with similar gene sets grouped close to each other. FDR, false discovery rate; GE, gene expression; KEGG, Kyoto Encyclopedia of Genes and Genomes; QOE, Qlucore Omics Explorer; VEGF, vascular endothelial growth factor.

Article Snippet: Qlucore Omics Explorer (QOE) version 3.1 software (Qlucore AB, Lund, Sweden) was used to analyze the differential expression of genes.

Techniques: Expressing