Computer Analysis IDs New IPF-halting Therapeutic Target

A computer analysis identified a tiny RNA molecule, or microRNA, as a potential therapeutic target to halt the progression of idiopathic pulmonary fibrosis (IPF), which was confirmed later in cell-based tests.

Researchers now plan to use these results to develop new RNA-based therapeutics or small molecules with the potential to treat fibrosis in human precision-cut lung slices, which have been used previously in preclinical studies.

These findings were reported in the study, “Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics,” published in the journal Nature Scientific Reports.

IPF is the most common form of interstitial lung disease (ILD), in which chronic inflammation and the progressive accumulation of certain components making up the network that surrounds and supports cells causes lung tissue to thicken and stiffen. Over time, this leads to the formation of scar tissue (fibrosis), making breathing difficult. 

Current therapies can slow IPF progression and prolong patients’ survival, but they cannot halt or reverse lung fibrosis. Thus, finding new underlying disease mechanisms and potential therapeutic targets are essential to improve treatment strategies.

RNA-binding proteins (RBPs) are a promising class of disease-related molecular targets, as they bind to many forms of RNA and perform various regulatory functions. 

Studies suggest RBPs play a role in fibrosis affecting the heart and orchestrate the formation of scar tissue. In particular, it has been found that increasing the production of an RBP called Quaking (QKI) had beneficial effects on heart fibrosis. However, whether QKI is therapeutically relevant in lung fibrosis is unknown.

One method to restore protein expression, or production, is to block small RNAs called microRNAs (miRNAs), which normally function in a regulatory fashion to suppress protein production. Therapeutically blocking miRNAs related to QKI may be a potential strategy to restore QKI activity and halt or reverse lung fibrosis.

To explore this possibility, a team of researchers led by Thomas Thum, MD, PhD, director of Fraunhofer ITEM and head of the Institute for Molecular and Translational Therapy Strategies at Hannover Medical School in Germany, applied a practical computer-based approach using multiple data sources to screen for miRNA candidates that could regulate QKI expression.

First, the team compared RNA sequence data from tissues isolated from 20 IPF patients to 19 control individuals to identify differentially expressed genes (DEGs), or genes with different activity levels. This screen yielded 4,451 DEGs which then were mapped onto 100 IPF-related genes to find those with higher activity (upregulated) or lower activity (downregulated) than controls.

These findings were cross-referenced with information on RBPs. This analysis identified 19 RBPs that were significantly deregulated in IPF tissues.

A similar comparison was conducted using whole gene expression data from human lung samples of 40 IPF patients and eight controls. This resulted in 1,206 DEGs and four deregulated RBPs.

In both independent datasets, QKI was confirmed to be downregulated, or less active, in IPF tissues compared with healthy tissues.

To investigate a potential regulatory role for QKI in IPF, the team searched for molecules that interacted with QKI (interactome) and found 45 interaction partners, of which 15 were significantly deregulated in IPF.

To validate these interactions, the team screened data from published single-cell RNA sequencing from 32 IPF patients and 28 controls. QKI expression was lower in various cell types, including fibroblasts and myofibroblasts, which are known to play a direct role in lung fibrosis.

Moreover, many of the molecules that interacted with QKI in the original screen also were deregulated in these cells, highlighting “a broad regulatory role of QKI and its predicted interactome in various cell types in IPF,” the team wrote.

Next, the team evaluated the susceptibility of QKI to miRNA-regulation, and found miRNA-506 had the potential to downregulate QKI and be involved in IPF.

“We have been focusing on microRNAs for 15 years already in our cardiovascular research, where they act as regulators of Quaking protein expression,” Thum said in a university press release. “This finding can now also be applied to the lungs: We have identified microRNA-506 as [a] regulator of Quaking.”

Computer-based results were confirmed in cell-based experiments using human lung fibroblasts. These experiments showed that QKI expression could be suppressed with the addition of miRNA-506 after a period of 48 hours.

Furthermore, after miR-506 treatment, lung fibroblasts had a significantly higher expression of genes known to be involved in fibrosis, “indicating the pro-fibrotic biological contribution of the miR-506-QKI axis,” the researchers wrote.

Finally, a large-scale analysis of proteins from human lung fibroblasts performed after miR-506 treatment found again that QKI was strongly suppressed. An additional assessment found 226 enriched functional processes and pathways associated with fibrosis, “pointing towards QKI as the likely key hub for miR-506 downstream effects.”

“In conclusion, we have confirmed a high potential of QKI-miR-506 axis involvement in lung fibrosis,” the investigators wrote, adding their findings also highlighted the utility of bioinformatic approaches to search for therapeutic targets for lung diseases and potentially other conditions.