Variability of gene expression profiles in human blood and lymphoblastoid cell lines
Background: Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up w...
| Main Authors: | , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
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BioMed Central
2010
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| author | Min, J Barrett, A Watts, T Pettersson, F Lockstone, H Lindgren, C Taylor, J Allen, M Zondervan, K McCarthy, M |
| author_facet | Min, J Barrett, A Watts, T Pettersson, F Lockstone, H Lindgren, C Taylor, J Allen, M Zondervan, K McCarthy, M |
| author_sort | Min, J |
| collection | OXFORD |
| description | Background: Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up whole blood can affect gene expression measurements. We therefore systematically investigated global gene expression profiles in peripheral blood from six individuals collected during two visits by comparing five of the following cell and RNA isolation methods: whole blood (PAXgene), peripheral blood mononuclear cells (PBMCs), lymphoblastoid cell lines (LCLs), CD19 and CD20 specific B-cell subsets. Results: Gene expression measurements were clearly discriminated by isolation method although the reproducibility was high for all methods (range ρ = 0.90-1.00). The PAXgene samples showed a decrease in the number of expressed genes (P < 1*10⁻¹⁶) compared to the other methods. Differentially expressed probes between PAXgene and PBMCs were correlated with the number of monocytes, lymphocytes, neutrophils or erythrocytes. The correlations (ρ = 0.83; ρ = 0.79) of the expression levels of detected probes between LCLs and B-cell subsets were much lower compared to the two B-cell isolation methods (ρ = 0.98). Gene ontology analysis of detected genes showed that genes involved in inflammatory responses are enriched in B-cells CD19 and CD20 whereas genes involved in alcohol metabolic process and the cell cycle were enriched in LCLs. Conclusion: Gene expression profiles in blood-based samples are strongly dependent on the predominant constituent cell type(s) and RNA isolation method. It is crucial to understand the differences and variability of gene expression measurements between cell and RNA isolation procedures, and their relevance to disease processes, before application in large clinical studies. |
| first_indexed | 2024-03-07T05:42:41Z |
| format | Journal article |
| id | oxford-uuid:e61b53c9-be25-4881-9deb-d5f909031bd5 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T05:42:41Z |
| publishDate | 2010 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:e61b53c9-be25-4881-9deb-d5f909031bd52022-03-27T10:29:00ZVariability of gene expression profiles in human blood and lymphoblastoid cell linesJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:e61b53c9-be25-4881-9deb-d5f909031bd5Medical SciencesBloodGenetics (medical sciences)EnglishOxford University Research Archive - ValetBioMed Central2010Min, JBarrett, AWatts, TPettersson, FLockstone, HLindgren, CTaylor, JAllen, MZondervan, KMcCarthy, MBackground: Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up whole blood can affect gene expression measurements. We therefore systematically investigated global gene expression profiles in peripheral blood from six individuals collected during two visits by comparing five of the following cell and RNA isolation methods: whole blood (PAXgene), peripheral blood mononuclear cells (PBMCs), lymphoblastoid cell lines (LCLs), CD19 and CD20 specific B-cell subsets. Results: Gene expression measurements were clearly discriminated by isolation method although the reproducibility was high for all methods (range ρ = 0.90-1.00). The PAXgene samples showed a decrease in the number of expressed genes (P < 1*10⁻¹⁶) compared to the other methods. Differentially expressed probes between PAXgene and PBMCs were correlated with the number of monocytes, lymphocytes, neutrophils or erythrocytes. The correlations (ρ = 0.83; ρ = 0.79) of the expression levels of detected probes between LCLs and B-cell subsets were much lower compared to the two B-cell isolation methods (ρ = 0.98). Gene ontology analysis of detected genes showed that genes involved in inflammatory responses are enriched in B-cells CD19 and CD20 whereas genes involved in alcohol metabolic process and the cell cycle were enriched in LCLs. Conclusion: Gene expression profiles in blood-based samples are strongly dependent on the predominant constituent cell type(s) and RNA isolation method. It is crucial to understand the differences and variability of gene expression measurements between cell and RNA isolation procedures, and their relevance to disease processes, before application in large clinical studies. |
| spellingShingle | Medical Sciences Blood Genetics (medical sciences) Min, J Barrett, A Watts, T Pettersson, F Lockstone, H Lindgren, C Taylor, J Allen, M Zondervan, K McCarthy, M Variability of gene expression profiles in human blood and lymphoblastoid cell lines |
| title | Variability of gene expression profiles in human blood and lymphoblastoid cell lines |
| title_full | Variability of gene expression profiles in human blood and lymphoblastoid cell lines |
| title_fullStr | Variability of gene expression profiles in human blood and lymphoblastoid cell lines |
| title_full_unstemmed | Variability of gene expression profiles in human blood and lymphoblastoid cell lines |
| title_short | Variability of gene expression profiles in human blood and lymphoblastoid cell lines |
| title_sort | variability of gene expression profiles in human blood and lymphoblastoid cell lines |
| topic | Medical Sciences Blood Genetics (medical sciences) |
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