Chest
Volume 141, Issue 3, March 2012, Pages 661-673
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Original Research
Pulmonary Vascular Disease
Gene Expression Profiling in the Lungs of Patients With Pulmonary Hypertension Associated With Pulmonary Fibrosis

https://doi.org/10.1378/chest.11-0449Get rights and content

Background

Pulmonary hypertension (PH) associated with pulmonary fibrosis (PF) is a severe condition with poor outcome. It is unknown whether patients with PF with associated PH (APH) represent a distinct phenotype of the disease. We hypothesized that the lung tissue gene expression pattern of patients with APH has a characteristic profile when compared with patients with PF without APH. We sought to determine if different gene expression signatures in PF could be determined based on pulmonary arterial pressures (PAPs) and to provide new insights into the pathobiology of APH.

Methods

Microarray analysis (Affymetrix) was performed after RNA was extracted from explanted lungs in 116 consecutive patients with PF (development set, n = 84; validation set, n = 32) and seven subjects with idiopathic pulmonary arterial hypertension undergoing lung transplant (LTx). PAP were recorded intraoperatively immediately before starting LTx. The development set was divided into three groups according to mean PAP (mPAP): severe PH group (mPAP ≥ 40 mm Hg, n = 17); intermediate PH group (mPAP 21-39 mm Hg, n = 45); NoPH group (mPAP ≤ 20 mm Hg, n = 22).

Results

Distinct gene signatures were observed. Patients in the severe PH group showed increased expression of genes, gene sets, and networks related to myofibroblast proliferation and vascular remodeling, whereas patients in the NoPH group strongly expressed proinflammatory genes. Two-dimensional hierarchic clustering based on 222 differentially expressed genes (severe PH vs no PH) dichotomized subjects into two phenotypes in the intermediate PH group and in the validation set. Real-time polymerase chain reaction confirmed the differential expression of selected genes.

Conclusions

Gene expression profiles distinguish PF phenotypes with and without APH. This observation can have important implications for future trials.

Section snippets

Subjects

One hundred sixteen fresh-frozen lung tissue specimens were obtained from the recipient organs of PF patients undergoing LTx. For the development analysis, the explanted lung specimens from 84 consecutive patients with PF (January 2001 to February 2007) were used (development set). For the validation analysis, lung specimens from 32 consecutive PF patients (March 2007 to October 2008) were analyzed (validation set) (Table 1). Systolic and diastolic pulmonary artery pressures (PAPs) were

SAM Identified Gene Signatures Based on PAP

The prevalence of PH (mPAP > 25 mm Hg) was 62% in the development set and 56% in the validation set (Table 1). There were no significant differences between the severe PH and the NoPH groups in terms of demographics and PFTs, with the exception of diffusing capacity of the lung for carbon monoxide (Dlco) (Table 2). Representative histologic slides from a patient with severe PH are showed in Figure 2.

SAM identified 222 differentially expressed genes between the severe PH and NoPH groups. One

Discussion

To our knowledge, this is the first study to compare the gene expression profiles of patients with PF and with and without APH. The high numerosity of the population studied allowed us to compare the “phenotypic extremes” in terms of PAP and to demonstrate that severe PH and NoPH groups of patients with PF exhibit distinct gene expression profiles. A mPAP ≥ 40 mm Hg is commonly considered as severe APH in patients with ILD,12, 22, 23 whereas an mPAP of 20 to 24 mm Hg may indicate borderline PH,

Conclusions

In conclusion, the gene expression signatures based on mPAP identified by microarray analysis in this study not only provide a rationale for the development of APH in a significant subset of patients with PF, but also identify an analytic framework to determine therapeutic targets for the treatment of APH. If validated at the protein level, gene expression signatures could potentially be used for patient selection in future trials for patients with PF.

Acknowledgments

Author contributions: Dr Mura takes responsibility for the integrity of the work as a whole, from inception to published article.

Dr Mura: contributed to the study concept and design, analysis and interpretation of the data, and drafting of the manuscript and review for important intellectual content.

Dr Anraku: contributed to the analysis and interpretation of the data and drafting of the manuscript and review for important intellectual content.

Ms Yun: contributed to the analysis and

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    Funding/Support: This study was supported by the Roche Multi Organ Transplant Academic Enrichment Fund and by the Lawson Scholarship.

    Reproduction of this article is prohibited without written permission from the American College of Chest Physicians (http://www.chestpubs.org/site/misc/reprints.xhtml).

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