Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples

Li Li, Lihua Ying, Maarten Naesens, Wenzhong Xiao, Tara Sigdel, Sue Hsieh, Jon Martin, Rong Chen, Kang Liu, Michael Mindrinos, Ron Davis, Minnie Sarwal

Research output: Contribution to journalArticlepeer-review

37 Scopus citations

Abstract

Microarray technology is a powerful tool in the discovery of new biomarkers for disease. After solid organ transplantation, where the detection of rejection is usually made on invasive biopsies, it could be hypothesized that noninvasive transcriptional profiling of peripheral blood will reveal rejection-specific expression patterns from circulating immune cells. However, in kidney transplant rejection, the analysis of gene expression data in whole blood has proven difficult for detecting significant genes specific for acute graft rejection. Previous studies have demonstrated that the abundance of globin genes in whole blood may mask the underlying biological differences between whole blood samples. In the present study, we compared the gene expression profiles of peripheral blood of nine stable renal allograft recipients with seven matched patients having an ongoing acute renal transplant rejection, using four different protocols of preparation, amplification, and synthesis of cRNA or cDNA and hybridization on the Affymetrix platform. We demonstrated that the globin reduction method is not sufficient to unmask clinically relevant rejection-specific transcriptome profiles in whole blood. Applying an additional mathematical depletion of the globin genes improves the efficacy of globin reduction but cannot remove the confounding influence of globin gene hybridization. Sampling of peripheral blood leukocytes alone, without the confounding influence of globin mRNA, provides sensitive and specific peripheral signatures for graft rejection, with many of these signals overlapping with rejection-driven tissue (kidney)-specific signatures from matched biopsies. Similar applications may exist for array-based biomarker discovery for other diseases associated with changes in leukocyte trafficking, activation, or function.

Original languageEnglish
Pages (from-to)190-197
Number of pages8
JournalPhysiological Genomics
Volume32
Issue number2
DOIs
StatePublished - 17 Jan 2008
Externally publishedYes

Keywords

  • Graft rejection
  • Kidney transplantation
  • Microarray analysis
  • Peripheral blood leukocytes

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