Healthy and idiopathic pulmonary fibrosis (IPF) lung cells respond differently to transforming growth factor-beta 1 (TGF-beta 1) — a key mediator of fibrosis — both in terms of gene activity and DNA methylation, likely due to the fibrotic environment that IPF cells are exposed to in the lungs, a study reports.
The study, “Transforming growth factor beta 1 induces methylation changes in lung fibroblasts,” was published in the journal PLOS ONE.
Yet, the genetic mechanisms underlying the influence of such environmental factors haven’t been extensively explored.
During IPF, the processes that are necessary to properly repair lung injuries become dysfunctional. Lung fibroblasts lose the ability to coordinate turning “on” (expressing) or turning “off” (silencing) genes involved in cell migration, proliferation, deposition of extracellular matrix, differentiation, and cell death. And the failure of this regulation has been associated with factors such as age and environment.
Alterations in DNA methylation are one of the best understood processes behind environment-driven genetic changes. They happen via so-called epigenetic effects, which refer to DNA modifications (in this case methylation) that do not change the DNA sequence but can affect the activity level of genes.
TGF-beta 1 is likely the strongest profibrotic mediator, and plays a critical role in the activation of fibroblasts (cells involved in tissue repair and fibrosis), but its effects on DNA methylation are not well known.
Therefore, a team of researchers sought to study how gene activity and DNA methylation profiles changed in normal versus IPF lung fibroblasts, following exposure to TGF-beta 1.
Fibroblasts were collected from biopsies in IPF patients or through surgery in healthy donors, and stimulated in the lab during a short (24 hours) or longer-term (five days) course of TGF-beta 1.
Using DNA chips, the researchers found changes in gene activity after short-term TGF-beta 1 induction, which were actually greater in normal fibroblasts compared to IPF fibroblasts.
Both fibroblast lines turned “on” genes involved in pathways related to the metabolism of lipids (fats), which have also been implicated in fibrosis (sterol regulatory element-binding proteins, SREBPs), as well as genes involved in the regulation of cell proliferation.
Conversely, TGF-beta 1 induced greater changes in DNA methylation after more prolonged stimulation (five days), and especially in IPF fibroblasts versus normal cells. The majority of observed alterations corresponded to loss of methylation (hypomethylation).
Consistent with these findings, TGF-beta 1 increased the amount of cell’s methylation machinery, including DNA methyltransferase 3 alpha (DMNT3a) and tet methylcytosine dioxygenase 3 (TET3) enzymes.
Using next-generation sequencing, the researchers were able to look at where exactly in the genome — an organism’s full set of DNA — these modifications in DNA methylation were happening.
They discovered that in normal fibroblasts, TGF-beta 1 mostly induced alterations at short DNA stretches, which are often found methylated, called “CpG islands.” On the other hand, in fibroblasts from IPF patients, alterations in DNA methylation were frequently seen elsewhere within genes.
Overall, the findings demonstrate that TGF-beta 1 “affects important elements of the DNA methylation/demethylation machinery (DNMT3a and TET3), and that IPF versus normal lung derived fibroblasts respond differently, likely because of the prior exposure to the fibrotic environment within the lung,” the researchers wrote.
Considering the genes whose activity was changed by TGF-beta 1, “these findings might suggest a possible role for therapeutic targeting of these pathways, however, more studies are needed,” the team added.