Ischemic stroke is a complex disease process with carotid atherosclerosis as the major etiologic source. To better understand the biology of a vulnerable plaque we carried out whole transcriptome shotgun sequencing of human carotid plaques.
Methods
5 carotid atherosclerotic plaques were obtained at the time of operation (2 symptomatic, 2 asymptomatic, and 1 control). RNA was isolated and 5 cDNA libraries were constructed and sequenced with single-reads100nt in length using one line of flow cell of HySeq 2000 (Illumina Inc). Standard bioinformatic techniques were used to ensure quality screening of raw reads. Ingenuity Systems IPA software was used to determine canonical biological pathways overrepresented in plaques. We compared our data to the data of Illumina Human Body Map processed by a similar analytical pipeline. Linkage analysis was performed.
Results
Among detected pathways were “Atherosclerosis Signaling” and pathways involved in inflammation and cell differentiation. We analyzed gene expression data by creating a distance matrix based on Jaccard similarity measure (Fig 1). When gene expression values were used to create a matrix of Euclidian distances between known transcriptomes, four specimens including the control clustered with heart and muscle. The transcriptome from the stroke patient was more similar to lung, liver and heart.
Conclusion
Whole transcriptome analysis of carotid plaques is feasible and ontologically accurate. We demonstrate linkage differences between symptomatic and asymptomatic plaques and biological pathways involved in vascular lesion formation. Further analysis may provide insight into the vulnerable plaque pathobiology.
Ligation of Macrophage Fcγ Receptors Recapitulates the Gene Expression Pattern of Vulnerable Human Carotid Plaques
