White blood cell differentials enrich whole blood expression data in the context of acute cardiac allograft rejection

Casey P Shannon, Zsuzsanna Hollander, Janet Wilson-McManus, Robert Balshaw, Raymond T Ng, Robert McMaster, Bruce M McManus, Paul A Keown, Scott J Tebbutt, Casey P Shannon, Zsuzsanna Hollander, Janet Wilson-McManus, Robert Balshaw, Raymond T Ng, Robert McMaster, Bruce M McManus, Paul A Keown, Scott J Tebbutt

Abstract

Acute cardiac allograft rejection is a serious complication of heart transplantation. Investigating molecular processes in whole blood via microarrays is a promising avenue of research in transplantation, particularly due to the non-invasive nature of blood sampling. However, whole blood is a complex tissue and the consequent heterogeneity in composition amongst samples is ignored in traditional microarray analysis. This complicates the biological interpretation of microarray data. Here we have applied a statistical deconvolution approach, cell-specific significance analysis of microarrays (csSAM), to whole blood samples from subjects either undergoing acute heart allograft rejection (AR) or not (NR). We identified eight differentially expressed probe-sets significantly correlated to monocytes (mapping to 6 genes, all down-regulated in ARs versus NRs) at a false discovery rate (FDR) ≤ 15%. None of the genes identified are present in a biomarker panel of acute heart rejection previously published by our group and discovered in the same data***.

Keywords: cell-specific expression; deconvolution; heart; microarray expression; transplantation.

Figures

Figure 1
Figure 1
Complete blood count leukocyte differentials reveal no statistically significant differences between groups in any cell sub-population. Note: (A–E) Relative abundance of white blood cell differential cell sub-populations in AR and NR subjects were plotted and their mean compared by a two-sided t-test.
Figure 2
Figure 2
Whole blood differential expression signal is reduced once we account for sample heterogeneity. Notes: (A and B) SAM in whole blood yields thousands of probe-sets differentially expressed at a relatively stringent FDR ≤ 5%. (C and D) Once sample heterogeneity is taken into account, the signal diminishes with only 1474 probe-sets called as differentially expressed at FDR ≤ 20%.
Figure 3
Figure 3
csSAM identifies cell type-specific differential expression in monocytes during acute cardiac allograft rejection. Notes: (A–F) Deconvolved differential expression analysis in the indicated cell types between samples from individuals either undergoing biopsy proven acute rejection or not. No significant probe-sets were identified in eosinophils or basophils (not shown).

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