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ProQR was founded in 2012 by chief executive officer (CEO) Daniel A. de Boer and co-founders Henri Termeer, Dinko Valerio and Gerard Platenburg.
The initial pipeline of the company was to develop small-molecule drugs or gene therapy that would treat cystic fibrosis (CF). Positive proof of concept (PoC) was achieved in 2016 with the clinical trial of the molecule QR-010 targeting the gene coding for cystic fibrosis transmembrane conductance regulator (CFTCR) in patients. Subsequently, the company expanded its pipeline into treating other rare diseases, including diseases of the eye.
In 2017, a spin-out of ProQR named Amylon Therapeutics was established in Leiden with the focus on the development of therapies for the central nervous system.
In 2021, ProQR announced a collaboration with Eli Lilly and Company on the Axiomer technology focused on "genetic disorders in the liver and nervous system". They signed a deal under which ProQR would receive US$ 50 million ($20 million upfront) and an equity investment of $30 million. The relationship between the two firms "deepened" in 2022 with expansion of the indications engagement and a $75 million cash infusion which included an equity stake.
In 2022, the company announced it would focus exclusively on advancing its RNA editing technology.