Expression profiling elucidates a molecular gene signature for pulmonary hypertension in sarcoidosis

Abstract

Pulmonary hypertension (PH), when it complicates sarcoidosis, carries a poor prognosis, in part because it is difficult to detect early in patients with worsening respiratory symptoms. Pathogenesis of sarcoidosis occurs via incompletely characterized mechanisms that are distinct from the mechanisms of pulmonary vascular remodeling well known to occur in conjunction with other chronic lung diseases. To address the need for a biomarker to aid in early detection as well as the gap in knowledge regarding the mechanisms of PH in sarcoidosis, we used genome-wide peripheral blood gene expression analysis and identified an 18-gene signature capable of distinguishing sarcoidosis patients with PH (n = 8), sarcoidosis patients without PH (n = 17), and healthy controls (n = 45). The discriminative accuracy of this 18-gene signature was 100% in separating sarcoidosis patients with PH from those without it. If validated in a large replicate cohort, this signature could potentially be used as a diagnostic molecular biomarker for sarcoidosis-associated PH.

Keywords: gene signature; peripheral blood mononuclear cells; pulmonary hypertension; sarcoidosis.

Figure 1

Enriched pathways among the differentially expressed genes between sarcoidosis patients with and those without pulmonary hypertension. The 20 top-ranked Kyoto Encyclopedia of Genes and Genomes pathways are listed. The red line indicates the cutoff of significance (0.05). MAPK: mitogen-activated protein kinase; VEGF: vascular endothelial growth factor.

Figure 2

A, Heat map of our 18-gene signature. Red represents increased gene expression, while blue represents gene expression. ++: sarcoidosis patients with PH; +: sarcoidosis patients without PH. B, C, Principal-component analysis (PCA); X-axis: first principal component (PC1); Y-axis: second principal component (PC2); left, PCA on the expression values of all the genes detected by microarray; right, PCA on the expression values of our 18-gene signature. PH: pulmonary hypertension/sarcoidosis patients with PH; Non-PH: sarcoidosis patients without PH. B, PCA on expression of the patients with and without PH. C, PCA on expression of the patients with and without PH and healthy controls. CTRL: healthy controls.

Figure S1

Heat map of 275 differentially expressed genes between sarcoidosis patients with (++) and those without PH (+). Red represents increased gene expression, while blue represents gene expression.

Figure S2

Enriched pathways among the differentially expressed genes between sarcoidosis patients without PH and healthy controls. The 20 top-ranked Kyoto Encyclopedia of Genes and Genomes pathways are listed. The red line indicates the cutoff of significance (0.05). VEGF: vascular endothelial growth factor; Jak-STAT: Janus kinase–signal transducers and activators of transcription.

Figure S3

Distribution of the classification accuracy in each recursive feature elimination (RFE) step. X-axis: number of genes in each step; Y-axis: classification accuracy from a 5-fold cross validation (repeated 1,000 times). The red line shows the average accuracy for each RFE step.