Whole blood transcriptomics identifies subclasses of pediatric septic shock

Abstract

Background Sepsis is a highly heterogeneous syndrome, which has hindered the development of effective therapies. This has prompted investigators to develop a precision medicine approach aimed at identifying biologically homogenous subgroups of patients with septic shock and critical illnesses. Transcriptomic analysis can identify subclasses derived from differences in underlying pathophysiological processes that may provide the basis for new targeted therapies. The goal of this study was to elucidate pathophysiological pathways and identify pediatric septic shock subclasses based on whole blood RNA expression profiles. Methods The subjects were critically ill children with cardiopulmonary failure who were a part of a prospective randomized insulin titration trial to treat hyperglycemia. Genome-wide expression profiling was conducted using RNA sequencing from whole blood samples obtained from 46 children with septic shock and 52 mechanically ventilated noninfected controls without shock. Patients with septic shock were allocated to subclasses based on hierarchical clustering of gene expression profiles, and we then compared clinical characteristics, plasma inflammatory markers, cell compositions using GEDIT, and immune repertoires using Imrep between the two subclasses. Results Patients with septic shock depicted alterations in innate and adaptive immune pathways. Among patients with septic shock, we identified two subtypes based on gene expression patterns. Compared with Subclass 2, Subclass 1 was characterized by upregulation of innate immunity pathways and downregulation of adaptive immunity pathways. Subclass 1 had significantly worse clinical outcomes despite the two classes having similar illness severity on initial clinical presentation. Subclass 1 had elevated levels of plasma inflammatory cytokines and endothelial injury biomarkers and demonstrated decreased percentages of CD4 T cells and B cells and less diverse T cell receptor repertoires. Conclusions Two subclasses of pediatric septic shock patients were discovered through genome-wide expression profiling based on whole blood RNA sequencing with major biological and clinical differences. Trial Registration This is a secondary analysis of data generated as part of the observational CAF-PINT ancillary of the HALF-PINT study (NCT01565941). Registered March 29, 2012.

Biological basis of critical illness subclasses: from the bedside to the bench and back again

“… 23 Pediatric Septic Shock Nanostring mRNA quantification Targeted assessment of Nrf2 linked genes identified greater downregulation among patients with endotype A, relative to patients with endotype B, suggestive of impaired antioxidant mechanisms Endotype specific responses will be retrospectively tested in patients enrolled in the Stress Hydrocortisone in Pediatric Septic Shock (SHIPPS, NCT0341398) - 96 subclass defining genes, 4 housekeeping genes Multi-center Observational Cohort N = 168 septic shock patients No controls 2. Yang et al 25 Whole blood derived RNA Subclass 1 and 2 Subclass 1 had overexpression of the innate immune arm and repression of the adaptive immune arm. Evidence of higher inflammatory cytokines and endothelial activation in Subclass 1 compared to Subclass 2 Subclass 1 had higher burden of organ failures when compared to Subclass 2.…”

“…Targeted analyses of nuclear factor erythroid-related factor 2 (Nrf2), a transcription factor that regulates expression of anti-oxidant genes, revealed greater downregulation among patients with endotype A . More recently among children with septic shock in secondary analyses of the Coagulation and Fibrinolysis in Pediatric Insulin Titration (CAF-PINT) study, Yang et al identified two septic shock subclasses using bulk mRNA sequencing 25 . Although the mortality among patients included in this cohort was low, Subclass 1 had higher burden or organ dysfunction compared to Subclass 2 and characterized by upregulation of the innate immune and downregulation of the adaptive immune pathways, with evidence of systemic inflammation and endothelial injury based on plasma protein biomarkers.…”

“…Deconvolution analyses of cellular composition suggested a decrease of CD4 T- and B-lymphocytes, and a lower diversity of T-cell receptors (TCR). 25 …”

Identification and transcriptomic assessment of latent profile pediatric septic shock phenotypes

“…Gene-expression profiling of whole blood has been used to identify sepsis subclasses [ 5 – 9 ]. Among children, Wong and colleagues used a 100 gene-expression panel, to identify pediatric septic shock Endotypes — A and B with prognostic value; assignment to Endotype A was associated with a nearly threefold increased risk of mortality, relative to those with Endotype B [ 10 ].…”