Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma

Daniel He,John-Paul Oliveria,Amrit Singh,Basak Sahin,Gail M Gauvreau,Casey P Shannon,Scott J Tebbutt,Chen Xi Yang

doi:10.1186/s13223-019-0382-x

Abstract

BackgroundBlood has proven to be a useful resource for molecular analysis in numerous biomedical studies, with peripheral blood mononuclear cells (PBMCs) and whole blood being the major specimen types. However, comparative analyses between these two major compartments (PBMCs and whole blood) are few and far between. In this study, we compared gene expression profiles of PBMCs and whole blood samples obtained from research subjects with or without mild allergic asthma.MethodsWhole blood (PAXgene) and PBMC samples were obtained from 5 mild allergic asthmatics and 5 healthy controls. RNA from both sample types was measured for expression of 730 immune-related genes using the NanoString nCounter platform.ResultsWe identified 64 uniquely expressed transcripts in whole blood that reflected a variety of innate, humoral, and adaptive immune processes, and 13 uniquely expressed transcripts in PBMCs which were representative of T-cell and monocyte-mediated processes. Furthermore, analysis of mild allergic asthmatics versus non-asthmatics revealed 47 differentially expressed transcripts in whole blood compared to 1 differentially expressed transcript in PBMCs (FDR < 0.25). Finally, through simultaneous measurement of PBMC proteins on the nCounter assay, we identified CD28 and OX40 (TNFRSF4), both of which are critical co-stimulatory molecules during T-cell activation, as significantly upregulated in asthmatics.ConclusionsWhole blood RNA preserved in PAXgene tubes is excellent for producing gene expression data with minimal variability and good sensitivity, suggesting its utility in multi-centre studies requiring measurement of blood gene expression.

Highlights

Blood has proven to be a useful resource for molecular analysis in numerous biomedical studies, with peripheral blood mononuclear cells (PBMCs) and whole blood being the major specimen types
Whole blood and PBMCs (Ficoll preparation) were obtained from 8 mild allergic asthmatics defined as skin test positive to common aeroallergens and having FEV1 ≤ 80% of predicted and methacholine PC20 ≤ 16 mg/ml, and 8 healthy controls at McMaster University (Hamilton, ON, Canada) (Table 1)
To examine overall gene expression, analysis of all measured transcripts on the NanoString Immune Profiling Panel (730 genes in total) revealed 704 differentially expressed genes (FDR < 0.25) between whole blood and PBMC compartments, of which only 6 genes (EGR1, IL32, FOS, CCL3L1, IFNL1, and EGR2) had increased levels of expression in PBMC samples compared to whole blood samples (Table 2; Fig. 1a, b)

Summary

Introduction

Blood has proven to be a useful resource for molecular analysis in numerous biomedical studies, with peripheral blood mononuclear cells (PBMCs) and whole blood being the major specimen types. We compared gene expression profiles of PBMCs and whole blood samples obtained from research subjects with or without mild allergic asthma. Allergic asthma has been described as a T helper type 2 (TH2) cell-mediated inflammatory response, characterized by airway and blood eosinophilia. While asthma can be controlled with corticosteroid treatment, some patients are steroid-resistant and require specific targeted therapies to manage their symptoms. This is more common in those with TH17-predominant asthma [4]

Methods

Results

Conclusion