Background
Methods
Definitions of the compared experimental conditions and models
In vitro experimental model | Experimental conditions | |||
---|---|---|---|---|
Model system | Unstimulated (“Ctr”) | 106/mL N. meningitidis (“Nm”) | 106/mL N. meningitidis + 25 ng/mL IL-10 (“Nm + IL-10”) | 25 ng/mL IL-10 (“IL-10”)a
|
Patient plasma system | Plasma from patients with meningococcal meningitis or mild meningococcemia (“low LPS plasma”) | Plasma from patients with severe meningococcal sepsis or septic shock, depleted for IL-10 (“IL-10 immunodepleted plasma”) | Plasma from patients with severe meningococcal sepsis or septic shock (“patient plasma with IL-10”) | Plasma from patients with meningococcal meningitis or mild meningococcemia, depleted for IL-10 (“low LPS plasma immunodepleted for IL-10”)a
|
Gene set enrichment analysis
Ingenuity pathway analysis
Canonical pathway analysis in IPA
Statistical analysis
Results
GSEA and IPA associated gene expression induced in the model system with similar sets of signaling pathways
Name of hallmark gene set | Descriptiona
| FDR | Number of genes in the gene set | Founder gene setsb
|
---|---|---|---|---|
Interferon alpha response | Genes up-regulated in response to alpha interferon proteins | <0.001 | 97 | 82 |
Interferon gamma response | Genes up-regulated in response to IFNG | <0.001 | 200 | 82 |
TNF signaling via NfkB | Genes regulated by NF-kB in response to TNF | <0.001 | 200 | 120 |
Inflammatory response | Genes defining inflammatory response | <0.001 | 200 | 120 |
Allograft rejection | Genes up-regulated during transplant rejection | <0.001 | 200 | 190 |
IL6 JAK-STAT3 signalling | Genes up-regulated by IL6 [via STAT3, e.g., during acute phase response] | <0.001 | 87 | 24 |
IL2 STAT5 signaling | Genes up-regulated by STAT5 in response to IL2 stimulation | <0.001 | 200 | 13 |
KRAS signaling down | Genes down-regulated by KRAS activation | <0.001 | 200 | 16 |
KRAS signaling up | Genes up-regulated by KRAS activation | <0.001 | 200 | 14 |
Apoptosis | Genes mediating programmed cell death (apoptosis) by activation of caspases | <0.001 | 161 | 80 |
Complement | Genes encoding components of the complement system, which is part of the innate immune system | 0.001 | 200 | 71 |
Epithelial mesenchymal transition | Genes defining epithelial-mesenchymal transition, as in wound healing, fibrosis and metastasis | 0.001 | 200 | 106 |
Coagulation | Genes encoding components of blood coagulation system; also up-regulated in platelets | 0.015 | 138 | 71 |
Estrogen response late | Genes defining late response to estrogen | 0.007 | 200 | 59 |
Hypoxia | Genes up-regulated in response to low oxygen levels (hypoxia) | 0.015 | 200 | 87 |
Name of hallmark gene set | Descriptiona
| FDR | Number of genes in the gene set | Founder gene setsb
|
---|---|---|---|---|
Interferon gamma response | Genes up-regulated in response to IFNG | <0.001 | 200 | 82 |
Interferon alpha response | Genes up-regulated in response to alpha interferon proteins. | <0.001 | 97 | 82 |
TNF signaling via NfkB | Genes regulated by NF-kB in response to TNF | <0.001 | 200 | 120 |
Inflammatory response | Genes defining inflammatory response | <0.001 | 200 | 120 |
IL2 STAT5 signaling | Genes up-regulated by STAT5 in response to IL2 stimulation. | <0.001 | 200 | 13 |
IL6 JAK-STAT3 signaling | Genes up-regulated by IL6 [via STAT3, e.g., during acute phase response] | <0.001 | 87 | 24 |
Allograft rejection | Genes up-regulated during transplant rejection | <0.001 | 200 | 190 |
Complement | Genes encoding components of the complement system, which is part of the innate immune system | <0.001 | 200 | 71 |
KRAS signaling up | Genes up-regulated by KRAS activation | 0.003 | 200 | 14 |
KRAS signaling down | Genes down-regulated by KRAS activation | 0.007 | 200 | 16 |
Apoptosis | Genes mediating programmed cell death (apoptosis) by activation of caspases | 0.007 | 161 | 80 |
Hypoxia | Genes up-regulated in response to low oxygen levels (hypoxia) | 0.039 | 200 | 87 |
GSEA and IPA associated gene expression induced in the patient plasma system with similar sets of signaling pathways
Name of hallmark gene set | Descriptiona
| FDR | Number of genes in the gene set | Founder gene setsb
|
---|---|---|---|---|
TNF signaling via NfkB | Genes regulated by NF-kB in response to TNF | <0.001 | 200 | 120 |
Inflammatory response | Genes defining inflammatory response. | <0.001 | 200 | 120 |
Interferon gamma response | Genes up-regulated in response to IFNG | <0.001 | 200 | 82 |
Interferon alpha response | Genes up-regulated in response to alpha interferon proteins. | <0.001 | 97 | 82 |
IL2 STAT5 signaling | Genes up-regulated by STAT5 in response to IL2 stimulation. | <0.001 | 200 | 13 |
IL6 JAK-STAT3 signaling | Genes up-regulated by IL6 [via STAT3, e.g., during acute phase response. | <0.001 | 87 | 24 |
KRAS signaling up | Genes up-regulated by KRAS activation. | 0.001 | 200 | 14 |
Epithelial mesenchymal transition | Genes defining epithelial-mesenchymal transition, as in wound healing, fibrosis and metastasis | <0.001 | 200 | |
Allograft rejection | Genes up-regulated during transplant rejection. | <0.001 | 200 | 190 |
MYC targets_v2 | A subgroup of genes regulated by MYC | 0.004 | 58 | 6 |
Complement | Genes encoding components of the complement system, which is part of the innate immune system. | 0.004 | 200 | 71 |
Coagulation | Genes encoding components of blood coagulation system | 0.005 | 138 | 71 |
Apoptosis | Genes mediating programmed cell death (apoptosis) by activation of caspases. | 0.016 | 161 | 80 |
Estrogen response early | Genes defining early response to estrogen | 0.018 | 200 | |
KRAS signaling down | Genes down-regulated by KRAS activation. | 0.029 | 200 | 16 |
Hypoxia | Genes up-regulated in response to low oxygen levels (hypoxia). | 0.031 | 200 | 87 |
UV response up | Genes up-regulated in response to ultraviolet (UV) radiation | 0.044 | 58 | 16 |
Name of hallmark gene set | Descriptiona
| FDR | Number of genes in the gene set | Founder gene setsb
|
---|---|---|---|---|
TNF signaling via NfkB | Genes regulated by NF-kB in response to TNF | <0.001 | 200 | 120 |
Interferon gamma response | Genes up-regulated in response to IFNG | <0.001 | 200 | 82 |
Inflammatory response | Genes defining inflammatory response | <0.001 | 200 | 120 |
Interferon alpha response | Genes up-regulated in response to alpha interferon proteins | <0.001 | 97 | 82 |
IL6 JAK-STAT3 signaling | Genes up-regulated by IL6 [via STAT3, e.g., during acute phase response] | <0.001 | 87 | 24 |
IL2 STAT5 signaling | Genes up-regulated by STAT5 in response to IL2 stimulation | <0.001 | 200 | 13 |
MYC targets_v2 | A subgroup of genes regulated by MYC | <0.001 | 58 | 6 |
Epithelial mesenchymal transition | Genes defining epithelial-mesenchymal transition, as in wound healing, fibrosis and metastasis | <0.001 | ||
Complement | Genes encoding components of the complement system | <0.001 | 200 | 71 |
Allograft rejection | Genes up-regulated during transplant rejection | <0.001 | 200 | 190 |
KRAS signaling up | Genes up-regulated by KRAS activation | 0.001 | 200 | 14 |
Estrogen response early | Genes defining early response to estrogen | 0.001 | ||
Coagulation | Genes encoding components of blood coagulation system | 0.001 | 138 | 71 |
UV response up | Genes up-regulated in response to ultraviolet (UV) radiation | 0.005 | 158 | 16 |
Hypoxia | Genes up-regulated in response to low oxygen levels (hypoxia) | 0.008 | 200 | 87 |
Apoptosis | Genes mediating programmed cell death (apoptosis) by activation of caspases | 0.013 | 161 | 80 |
Unfolded protein response | Genes up-regulated during unfolded protein response, a cellular stress response related to the endoplasmic reticulum | 0.036 | 113 | 22 |
Gene set enrichment analysis identified genes differentially induced by IL-10 to be associated with similar gene sets in both the model system and the patient plasma system
Gene sets enriched in Nm + IL-10 vs Nm | Gene sets enriched in patient plasma with IL-10 vs IL-10 immunodepleted plasma | Gene sets enriched in Nm vs Nm + IL-10 | Gene sets enriched in IL-10 immunodepleted plasma vs patient plasma with with IL-10 |
---|---|---|---|
Oxidative phosphorylation | Oxidative phosphorylation | TNF signaling | Interferon alpha response |
MYC Targets_v1 | Peroxisome | KRAS signaling DN | TNF signaling |
DNA repair | MYC Targets_v1 | Epithelial-mesenchymal transition | UV response |
Adipogenesis | Adipogenesis | UV response | Interferon gamma response |
Peroxisome | MYC targets_v2 | Inflammatory response | Allograft rejection |
MYC targets_v2 | P53 Pathway | Kras signaling up | Kras signaling up |
P53 Pathway | Reactive oxygen species | Apical surface | Hedgehog signaling |
Protein secretion | DNA repair | Cholesterol homeostasis | Hallmark angiogenesis |
Fatty Acid Metabolism | Allograft rejection | Mitotic spindle | |
Glycolysis | Interferon alpha response | ||
Bile acid metabolism | Coagulation |
GSEA and IPA identified significant down-regulation of genes associated with mitochondrial function and oxidative phosphorylation in human monocytes stimulated by meningococcal LPS, and partial up-regulation of this response by IL-10
Symbol | Entrez gene name | Location | Type(s) | Fold change1
| ||
---|---|---|---|---|---|---|
Nm vs ctr | Nm + IL-10 vs ctr | Nm + IL-10 vs Nm | ||||
ACO2 | aconitase 2, mitochondrial | Cytoplasm | Enzyme | −1.66 | −1.33 | 1.25 |
ATP5A1 | ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle | Cytoplasm | Transporter | −1.83 | −1.34 | 1.37 |
ATP5H | ATP synthase, H+ transporting, mitochondrial Fo complex, subunit d | Cytoplasm | Enzyme | −1.50 | −1.18 | 1.27 |
BCL2 | B-cell CLL/lymphoma 2 | Cytoplasm | Transporter | NC | NC | −1.46 |
CASP3 | caspase 3, apoptosis-related cysteine peptidase | Cytoplasm | Peptidase | NC | 1.86 | 1.79 |
COX7C | cytochrome c oxidase subunit VIIc | Cytoplasm | Enzyme | −1.66 | NC | 1.45 |
CYB5A | cytochrome b5 type A (microsomal) | Cytoplasm | Enzyme | −1.69 | NC | 1.48 |
FURIN | furin (paired basic amino acid cleaving enzyme) | Cytoplasm | Peptidase | −2.47 | 1.42 | 3.51 |
NCSTN | nicastrin | Plasma Membrane | Peptidase | −1.41 | 1.17 | 1.21 |
NDUFA6 | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14 kDa | Cytoplasm | Enzyme | −2.00 | −1.53 | 1.31 |
NDUFA9 | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39 kDa | Cytoplasm | Enzyme | 1.28 | 3.10 | 2.43 |
NDUFA10 | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42 kDa | Cytoplasm | Transporter | −1.38 | −1.14 | 1.22 |
NDUFAB1 | NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8 kDa | Cytoplasm | Enzyme | −2.26 | −1.56 | 1.45 |
NDUFB5 | NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16 kDa | Cytoplasm | Enzyme | −1.48 | NC | 1.37 |
NDUFS2 | NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49 kDa (NADH-coenzyme Q reductase) | Cytoplasm | Enzyme | −2.04 | NC | 1.92 |
NDUFS6 | NADH dehydrogenase (ubiquinone) Fe-S protein 6, 13 kDa (NADH-coenzyme Q reductase) | Cytoplasm | Enzyme | −1.74 | −1.42 | 1.22 |
NDUFV2 | NADH dehydrogenase (ubiquinone) flavoprotein 2, 24 kDa | Cytoplasm | Enzyme | NC | −1.61 | −1.44 |
PRDX3 | peroxiredoxin 3 | Cytoplasm | Enzyme | −1.63 | NC | 1.47 |
SDHB | succinate dehydrogenase complex, subunit B, iron sulfur (Ip) | Cytoplasm | Enzyme | −1.91 | −1.41 | 1.35 |
TRAK1 | trafficking protein, kinesin binding 1 | Nucleus | Other | −1.29 | NC | 1.25 |
UCP2 | uncoupling protein 2 (mitochondrial, proton carrier) | Cytoplasm | Transporter | −2.07 | −1.49 | 1.39 |
UQCR10 | ubiquinol-cytochrome c reductase, complex III subunit X | Cytoplasm | Enzyme | −1.75 | −1.38 | 1.26 |
VPS9D1 | VPS9 domain containing 1 | Other | Transporter | NC | NC | 1.86 |