Link to the University of Pittsburgh Homepage
Link to the University Library System Homepage Link to the Contact Us Form

Characterization of whole blood gene expression profiles as a sequel to globin mRNA reduction in patients with sickle cell disease

Raghavachari, N and Xu, X and Munson, PJ and Gladwin, MT (2009) Characterization of whole blood gene expression profiles as a sequel to globin mRNA reduction in patients with sickle cell disease. PLoS ONE, 4 (8).

[img]
Preview
PDF
Published Version
Available under License : See the attached license file.

Download (598kB) | Preview
[img] Plain Text (licence)
Available under License : See the attached license file.

Download (1kB)

Abstract

Global transcriptome analysis of whole blood RNA using microarrays has been proven to be challenging due to the high abundance of globin transcripts that constitute 70% of whole blood mRNA. This is a particular problem in patients with sickle cell disease, secondary to the high abundance of globin-expressing nucleated red blood cells and reticulocytes in the circulation. In order to accurately measure the steady state blood transcriptome in sickle cell patients we evaluated the efficacy of reducing globin transcripts in PAXgene stabilized RNA for genome-wide transcriptome analyses using microarrays. We demonstrate here by both microarrays and Q-PCR that the globin mRNA depletion method resulted in 55-65 fold reduction in globin transcripts in whole blood collected from healthy volunteers and sickle cell disease patients. This led to an improvement in microarray data quality by reducing data variability, with increased detection rate of expressed genes and improved overlap with the expression signatures of isolated peripheral blood mononuclear (PBMC) preparations. Analysis of differences between the whole blood transcriptome and PBMC transcriptome revealed important erythrocyte genes that participate in sickle cell pathogenesis and compensation. The combination of globin mRNA reduction after whole-blood RNA stabilization represents a robust clinical research methodology for the discovery of biomarkers for hematologic diseases.


Share

Citation/Export:
Social Networking:
Share |

Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Raghavachari, N
Xu, X
Munson, PJ
Gladwin, MTmtg16@pitt.eduMTG16
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorCreighton, ChadUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Date: 3 August 2009
Date Type: Publication
Journal or Publication Title: PLoS ONE
Volume: 4
Number: 8
DOI or Unique Handle: 10.1371/journal.pone.0006484
Schools and Programs: School of Medicine > Critical Care Medicine
Refereed: Yes
MeSH Headings: Anemia, Sickle Cell--blood; Anemia, Sickle Cell--genetics; Electrophoresis, Polyacrylamide Gel; Gene Expression Profiling; Globins--genetics; Humans; Oligonucleotide Array Sequence Analysis; RNA, Messenger--genetics; Reverse Transcriptase Polymerase Chain Reaction
PubMed Central ID: PMC2714456
PubMed ID: 19649296
Date Deposited: 03 Aug 2012 15:08
Last Modified: 04 Feb 2019 15:59
URI: http://d-scholarship.pitt.edu/id/eprint/13159

Metrics

Monthly Views for the past 3 years

Plum Analytics

Altmetric.com


Actions (login required)

View Item View Item