Microarray profiling reveals suppressed interferon stimulated gene program in fibroblasts from scleroderma-associated interstitial lung disease

Abstract

BackgroundInterstitial lung disease is a major cause of morbidity and mortality in systemic sclerosis (SSc), with insufficiently effective treatment options. Progression of pulmonary fibrosis involves expanding populations of fibroblasts, and the accumulation of extracellular matrix proteins. Characterisation of SSc lung fibroblast gene expression profiles underlying the fibrotic cell phenotype could enable a better understanding of the processes leading to the progressive build-up of scar tissue in the lungs. In this study we evaluate the transcriptomes of fibroblasts isolated from SSc lung biopsies at the time of diagnosis, compared with those from control lungs.MethodsWe used Affymetrix oligonucleotide microarrays to compare the gene expression profile of pulmonary fibroblasts cultured from 8 patients with pulmonary fibrosis associated with SSc (SSc-ILD), with those from control lung tissue peripheral to resected cancer (n=10). Fibroblast cultures from 3 patients with idiopathic pulmonary fibrosis (IPF) were included as a further comparison. Genes differentially expressed were identified using two separate analysis programs following a set of pre-determined criteria: only genes significant in both analyses were considered. Microarray expression data was verified by qRT-PCR and/or western blot analysis.ResultsA total of 843 genes were identified as differentially expressed in pulmonary fibroblasts from SSc-ILD and/or IPF compared to control lung, with a large overlap in the expression profiles of both diseases. We observed increased expression of a TGF-β response signature including fibrosis associated genes and myofibroblast markers, with marked heterogeneity across samples. Strongly suppressed expression of interferon stimulated genes, including antiviral, chemokine, and MHC class 1 genes, was uniformly observed in fibrotic fibroblasts. This expression profile includes key regulators and mediators of the interferon response, such as STAT1, and CXCL10, and was also independent of disease group.ConclusionsThis study identified a strongly suppressed interferon-stimulated gene program in fibroblasts from fibrotic lung. The data suggests that the repressed expression of interferon-stimulated genes may underpin critical aspects of the profibrotic fibroblast phenotype, identifying an area in pulmonary fibrosis that requires further investigation.

Interstitial lung disease

“…It can be hypothesised that this suppression could enhance lung fibrosis progression through fibroblast proliferation and apoptosis resistance. Interestingly, suppression of interferon-stimulated genes has also been observed in cancers representing one more similarity between fibrogenesis and tumorigenesis [103].…”

“…It is believed that targeting lung fibroblasts may be an important step for future treatment. A recent mRNA microarray study of lung fibroblasts in SSc-associated NSIP has produced important findings [103]. First, a similarity in gene expression profile with IPF has been observed and a drug targeting fibroblasts may be effective in both diseases.…”

Management of Systemic-Sclerosis-Associated Interstitial Lung Disease

“…Although not completely concordant, lung tissue gene expression and bronchoalveolar lavage (BAL) studies of early and late-stage SSc-ILD demonstrate abnormal expression of markers of macrophage migration and activation, as well as up-regulated expression of TGF-β and interferon-regulated genes. 4–6 Genome wide association studies have found the gene for CXCL4 (chemokine [C-X-C motif] ligand 4), among others, to be highly and differentially expressed in certain SSc patients, and a recent proteome-wide analysis found serum levels of CXCL4 to be correlated with lung fibrosis. 7 Polymorphisms at loci for additional genes have also been reported to be associated with the presence and/or severity of pulmonary fibrosis (see Table 1).…”

Interstitial lung disease in systemic sclerosis: where do we stand?

“…Lower levels of thymosin β-4 in the bronchoalveolar lavage of SSc-ILD patients have been correlated with disease progression [14]. In recent years, some genetic studies have shown increased expression of the TGF-β response including fibrosis-associated genes and myofibroblast markers [15,16]. An analysis of gene expression in skin biopsies identified some transcripts that correlate with the severity of SSc-ILD.…”