Whole blood transcriptomics identifies subclasses of pediatric septic shock
Authors: Yang Jamie O. , Zinter Matt S. , Pellegrini Matteo , Wong Man Yee , Gala Kinisha , Markovic Daniela , Nadel Brian , Peng Kerui , Do Nguyen , Mangul Serghei , Nadkarni Vinay M. , Karlsberg Aaron , Deshpande Dhrithi , Butte Manish J. , Asaro Lisa , Agus Michael , Sapru Anil ,   Study Site Investigators for CAF-PINT, Agus Michael , Srinivasan Vijay , Chima Ranjit S. , Neal Neal J. , Newth Christopher , Hassinger Amanda B. , Bysani Kris , Faustino Edward Vincent , Hirshberg Faustino , Wintergerst Kupper , Sullivan Janice E. , Schwarz Adam , Sorce Lauren , Marsillio Lauren , Cvijanovich Natalie , Flori Heidi , Pham Flori , Dahmer Mary , Federman Myke , Wong Kayley , Vangala Sitaram S. , Pellegrini Matteo , Balliu Brunilda , Gala Kinisha P. , Nett Sholeen , Singleton Marcy , Pinto Neethi , Chong Grace , Viteri Shirley , Sapru Anil , McQuillen Patrick , Zinter Matt , Coughlin-Wells Kerry , Hughes Kyle , French Jaclyn , Fitzgerald Meghan , Sisko Martha , Howard Kelli , Jones Rhonda , Spear Debbie , Eldridge Peter , Kwok Jeni , Qiao Haiping , Monjure Tracey , Tala Joana , Kandil Sarah A. , Quinn Tyler , Lilley Jennifer , Lee Kristen , Flores Cathy , Vargas-Shiraishi Ofelia , Shukla Avani , Brumfield Becky , Stone Cheryl , Jayachandran Chaandini , Kirkpatrick Theresa , Deshmukh Tanaya , Mareboina Manvita , Do Nguyen , Ashtari Neda , Ratiu Anna , Jarvis Dean , McNally Mary , Martini Karlyn , Rodgers Chiara , John Ramany , Mulholland Teresa , Pellicciotti Gwen , Goel Shrey , Alkhouli Mustafa , McKenzie Anne , Villarreal-Chico Denise 
Published: December 2023

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.