Development of RNA aptamers targeting the NADPH oxidase DUOX1 as a therapeutic approach to treat lung fibrosis – APFIBROX

The SELEX method involves selecting aptamers bound to a target expressed on the cell surface. This required first identifying the optimal conditions for cell adhesion to the substrate. A library of RNA aptamers (10¹⁵ molecules) chemically modified to make them resistant was incubated with cells whose surface expression of DUOX1 is induced by an antibiotic. Initially, the library was incubated with cells not expressing DUOX1 to eliminate non-specifically bound aptamers. The unbound molecules were then recovered and incubated with DUOX1-expressing cells. The cell-bound aptamers were then recovered and re-amplified to generate a new pool of aptamers, which was used for a new selection cycle. In each selection cycle, the aptamers were analyzed by sequencing and grouped into families. Enriching these families allowed for the identification of potential aptamers. These were then analyzed for their ability to inhibit the ROS-generating activity of DUOX1 and to inhibit the activation of the cell signaling pathway that controls fibrogenesis in fibroblasts isolated from mouse lungs.

During this project, 33 promising candidate aptamers were identified. Of these 33 aptamers, two were selected based on their ability to inhibit DUOX1 activity. To determine the crucial elements of their respective sequences involved in DUOX1 recognition, two new variant libraries of these two aptamers, containing 10% mutations, were synthesized and used for two cycles of SELEX. Enrichment analysis showed that, among the two aptamers, the Dx1781 aptamer exhibited significantly higher enrichment and thus appeared promising. Incubation of this aptamer with mouse fibroblasts showed that it inhibited the activation of the TGF-beta pathway, a major pathway in fibrosis.

Chronic respiratory diseases, including lung fibrosis are a major and increasing burden in terms of morbidity and mortality. Lung fibrosis is characterized by excessive matrix deposition leading to destruction of lung architecture and ultimately fatal impairment of lung function. Idiopathic pulmonary fibrosis (IPF) is the most common form of lung fibrosis, carrying a high mortality rate with 3-years median survival after diagnosis. IPF results from an aberrant activation of alveolar epithelial cells that provokes excessive migration, proliferation and activation of fibroblasts with the formation of (myo)fibroblastic foci and excessive deposition of extracellular matrix. The need to develop innovative treatments for pulmonary fibrosis has emerged as an important therapeutic challenge.
A growing body of evidence supports the hypothesis that a chronic oxidative stress might serve to drive the progression of fibrosis. Reactive Oxygen Species (ROS) and markers of oxidative stress are evident in human IPF and levels of ROS negatively correlate with pulmonary function in IPF and may predict disease severity. Cells can produce ROS through activation and/or induction of NADPH oxidases (NOX), which constitute a family of “professional” membrane-bound ROS-generating enzymes. This family consists of seven members, five NOXs (NOX1-5) and two dual oxidases (DUOX1 and 2).
The DUOXs are plasma membrane-targeted H2O2 generators. Our in vivo data (IPF patients, mice models of lung fibrosis) show that DUOX1 is induced in response to lung injury. In addition to be highly expressed at the epithelial surface of the airways, DUOX1 is also well expressed in myofibroblastic foci of the remodeled IPF lung. DUOX1-deficient mice (DUOX1+/- and DUOX1-/-) are protected from drug- and radio-induced lung fibrosis. Analysis of the mechanism revealed a new function for DUOX1-derived H2O2 as a signalling amplifier of the TGF-B1 pathway that causes a chronic long-term fibroblast activation, contributing thus to unrestrained and progressive fibrosis. These new data provide proof of concept for therapeutic targeting of DUOX1 in fibrotic lung disorders. At present, no specific DUOXs inhibitors exist. Hence, the overall objective of this project is to develop an innovative therapeutic strategy to counteract progression of lung fibrosis, based on the use of aptamers. These molecules are oligonucleotides (DNA or RNA) that can fold into complex 3D structures and bind to targets with high affinity and specificity based on shape complementarity thus inhibiting their function. Several aptamer therapeutics for other diseases have now shown promise in clinical trials.
The project is divided into three key tasks: Task1: selection of nuclease resistant 2’Fluoro-Pyrimidine RNA aptamers against DUOX1 molecules by using whole cell SELEX strategy. To this end, the DUOX1-inducible HEK293 cell line will be used for the selection, Task 2: Identification and functional characterization of aptamers candidates by analyzing their ability to inhibit both human and murine TGF-B1 induced myofibroblastic differentiation process by using mouse and patient-derived lung fibroblasts and Task3: evaluation of the therapeutic efficacy of selected aptamers by using a bleomycin-induced pulmonary fibrosis mouse model.
We expect to identify aptamer(s) against DUOX1 as promising therapeutic tools with the potential to counteract the pathological process of this deadly chronic lung disease with increasing clinical and economic burden. In addition, while writing this funding application, we also became aware that severe pulmonary fibrosis can be induced by the new coronavirus, SARS-CoV-2. Accordingly, we believe that these aptamers could also be useful to reduce lung fibrosis in other pathologies.
This project brings together 2 teams (C. Dupuy and F. Ducongé) and their know-how, which are highly complementary, associating expertise in oxidative stress and NADPH oxidases and Aptamers.