Genomic expression profiling across the pediatric systemic inflammatory response syndrome, sepsis, and septic shock spectrum

Abstract

Objectives: To advance our biological understanding of pediatric septic shock, we measured the genome-level expression profiles of critically ill children representing the systemic inflammatory response syndrome (SIRS), sepsis, and septic shock spectrum.

Design: Prospective observational study involving microarray-based bioinformatics.

Setting: Multiple pediatric intensive care units in the United States.

Patients: Children <or=10 years of age: 18 normal controls, 22 meeting criteria for SIRS, 32 meeting criteria for sepsis, and 67 meeting criteria for septic shock on day 1. The available day 3 samples included 20 patients still meeting sepsis criteria, 39 patients still meeting septic shock criteria, and 24 patients meeting the exclusive day 3 category, SIRS resolved.

Interventions: None other than standard care.

Measurements and main results: Longitudinal analyses were focused on gene expression relative to control samples and patients having paired day 1 and day 3 samples. The longitudinal analysis focused on up-regulated genes revealed common patterns of up-regulated gene expression, primarily corresponding to inflammation and innate immunity, across all patient groups on day 1. These patterns of up-regulated gene expression persisted on day 3 in patients with septic shock, but not to the same degree in the other patient classes. The longitudinal analysis focused on down-regulated genes demonstrated gene repression corresponding to adaptive immunity-specific signaling pathways and was most prominent in patients with septic shock on days 1 and 3. Gene network analyses based on direct comparisons across the SIRS, sepsis, and septic shock spectrum, and all available patients in the database, demonstrated unique repression of gene networks in patients with septic shock corresponding to major histocompatibility complex antigen presentation. Finally, analyses focused on repression of genes corresponding to zinc-related biology demonstrated that this pattern of gene repression is unique to patients with septic shock.

Conclusions: Although some common patterns of gene expression exist across the pediatric SIRS, sepsis, and septic shock spectrum, septic shock is particularly characterized by repression of genes corresponding to adaptive immunity and zinc-related biology.

Figure 1

A, Venn analysis comparing the day 1 genes differentially regulated between the respective patient categories and the control subjects (see Table 2). B, Venn analysis comparing the day 3 genes differentially regulated between the respective patient categories and the control subjects (see Table 2). SIRS, systemic inflammatory response syndrome.

Figure 2

Gene network derived from the 136 genes differentially regulated on day 1 between patients with systemic inflammatory response syndrome (SIRS), sepsis, and septic shock (see text for derivation of the 136 genes and for network derivation). Red intensity within a gene node corresponds to increased expression in the patients with septic shock, relative to the patients with SIRS or sepsis, and green intensity within a gene node corresponds to decreased expression in the patients with septic shock, relative to the patients with SIRS or sepsis. This network has a score of 54, which is equivalent to a p value of 1.0E–54. The p value provides an estimate of the probability that the network genes are present in the uploaded gene list by chance alone. A network legend and a complete list of the network genes are provided in Supplemental Digital Content 5, http://links.lww.com/A1104. HLA, human leukocyte antigen; MHC, major histocompatibility complex; IFN, interferon; IL, interleukin; IGHM, immunoglobulin heavy constant mu; UHRF, ubiquitin-like with PHD and ring finger domains 1; LDLR, low density lipoprotein receptor; AGTRAP, angiotensin II receptor-associated protein; CCNB, cyclin B2; RETN, resistin; HMMR, hyaluronan-mediated motility receptor (RHAMM); HDAC, histone deacetylase 9; MAPK, mitogen activated protein kinase; ERK, extracellular regulated MAP kinase; JNK, jun n-terminal kinase; TRIB, tribbles homolog 1; MEF, myocyte enhancer factor.

Figure 3

The first gene network derived from the 535 genes differentially regulated on day 3 between patients with systemic inflammatory response syndrome (SIRS) resolved, sepsis, and septic shock (see text for derivation of the 535 genes and for network derivation). Red intensity within a gene node corresponds to increased expression in the patients with septic shock, relative to the patients with SIRS resolved or sepsis, and green intensity within a gene node corresponds to decreased expression in the patients with septic shock, relative to the patients with SIRS resolved or sepsis. This network has a score of 36, which is equivalent to a p value of 1.0E–36. The p value provides an estimate of the probability that the network genes are present in the uploaded gene list by chance alone. A network legend and a complete list of the network genes are provided in Supplemental Digital Content 6, http://links.lww.com/A1105. HLA, human leukocyte antigen; MHC, major histocompatibility complex; IFN, interferon; IL, interleukin; RFX, regulatory factor X; CST, cystatin F; CARD, caspase recruitment domain family, member 6; CXCL, chemokine (C-X-C motif) ligand 16; GOS, G0/G1 switch 2; MYBL, v-myb myeloblastosis viral oncogene homolog; KLRG, killer cell lectin-like receptor subfamily G, member 1; BTLA, B and T lymphocyte associated; GAB, GRB2-associated binding protein 2; PLC, phospholipase C gamma; SOCS, suppressor of cytokine signaling 3; SIRPA, signal-regulatory protein alpha; LLRA, leukocyte immunoglobulin-like receptor, subfamily A; FCER, Fc fragment of IgE, high affinity I; FCAR, Fc fragment of IgA; KLRB, killer cell lectin-like receptor subfamily B, member 1.

Figure 4

The second gene network derived from the 535 genes differentially regulated on day 3 between patients with systemic inflammatory response syndrome (SIRS) resolved, sepsis, and septic shock (see text for derivation of the 535 genes and for network derivation). Red intensity within a gene node corresponds to increased expression in the patients with septic shock, relative to the patients with SIRS resolved or sepsis, and green intensity within a gene node corresponds to decreased expression in the patients with septic shock, relative to the patients with SIRS resolved or sepsis. This network has a score of 43, which is equivalent to a p value of 1.0E–43. The p value provides an estimate of the probability that the network genes are present in the uploaded gene list by chance alone. A network legend and a complete list of the network genes are provided in Supplemental Digital Content 7, http://links.lww.com/A1106. TNF, tumor necrosis factor; MMP, matrix metalloproteinase; IL, interleukin; TGF, transforming growth factor; TIMP, TIMP metallopeptidase inhibitor; RECK, reversion-inducing-cysteine-rich protein with kazal motifs; LRG, leucine-rich alpha-2-glycoprotein 1; RUNX, runt-related transcription factor 2; SMURF, SMAD specific E3 ubiquitin protein ligase 1; FUT, fucosyltransferase 7; NOC, nucleolar complex associated 3 homolog; CCR, chemokine (C-C motif) receptor 6; ITGA, integrin, alpha 7; ALPL, alkaline phosphatase, liver/bone/kidney; PDLIM, PDZ and LIM domain 7; MBNL, muscleblind-like 2; DAHC, dachshund homolog 1; WWP, WW domain containing E3 ubiquitin protein ligase 2; FDNC, fibronectin type III domain containing 3B.