Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma
Abstract Background 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. However, comparative analyses between these two major compartments (PBMCs and whole bloo...
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doaj-60d462d4945546638e5e2d7741d0e84a2020-11-25T04:09:53ZengBMCAllergy, Asthma & Clinical Immunology1710-14922019-11-0115111010.1186/s13223-019-0382-xWhole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthmaDaniel He0Chen Xi Yang1Basak Sahin2Amrit Singh3Casey P. Shannon4John-Paul Oliveria5Gail M. Gauvreau6Scott J. Tebbutt7Centre for Heart Lung Innovation, University of British ColumbiaCentre for Heart Lung Innovation, University of British ColumbiaCentre for Heart Lung Innovation, University of British ColumbiaCentre for Heart Lung Innovation, University of British ColumbiaPrevention of Organ Failure (PROOF) Centre of ExcellenceDepartment of Medicine, McMaster UniversityDepartment of Medicine, McMaster UniversityCentre for Heart Lung Innovation, University of British ColumbiaAbstract Background 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. 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. Methods Whole 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. Results We 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. Conclusions Whole 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.http://link.springer.com/article/10.1186/s13223-019-0382-xWhole bloodPBMCGene expressionAsthma |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Daniel He Chen Xi Yang Basak Sahin Amrit Singh Casey P. Shannon John-Paul Oliveria Gail M. Gauvreau Scott J. Tebbutt |
spellingShingle |
Daniel He Chen Xi Yang Basak Sahin Amrit Singh Casey P. Shannon John-Paul Oliveria Gail M. Gauvreau Scott J. Tebbutt Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma Allergy, Asthma & Clinical Immunology Whole blood PBMC Gene expression Asthma |
author_facet |
Daniel He Chen Xi Yang Basak Sahin Amrit Singh Casey P. Shannon John-Paul Oliveria Gail M. Gauvreau Scott J. Tebbutt |
author_sort |
Daniel He |
title |
Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma |
title_short |
Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma |
title_full |
Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma |
title_fullStr |
Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma |
title_full_unstemmed |
Whole blood vs PBMC: compartmental differences in gene expression profiling exemplified in asthma |
title_sort |
whole blood vs pbmc: compartmental differences in gene expression profiling exemplified in asthma |
publisher |
BMC |
series |
Allergy, Asthma & Clinical Immunology |
issn |
1710-1492 |
publishDate |
2019-11-01 |
description |
Abstract Background 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. 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. Methods Whole 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. Results We 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. Conclusions Whole 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. |
topic |
Whole blood PBMC Gene expression Asthma |
url |
http://link.springer.com/article/10.1186/s13223-019-0382-x |
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