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This prospectus relates to the proposed resale or other disposition, from time to time, in one or moreofferings, of up to 3,523,538 ordinary shares, nominal value €0.04 per share (the “Shares”), by the sellingshareholder identified in this prospectus (the “Selling Shareholder”). The Shares to which this prospectusrelates were issued to the Selling Shareholder pursuant to that certain Share Purchase Agreement, dated asof October22, 2024 (the “Share Purchase Agreement”), that we entered into as part of a private placementinvolving the Selling Shareholder, as further described in this prospectus. We are registering the resale of our ordinary shares covered by this prospectus as required by theregistration rights granted under the Share Purchase Agreement. Our registration of the Shares covered bythis prospectus does not mean that the Selling Shareholder will offer or sell any of the Shares nor does itrequire us to issue any of our ordinary shares. We are not selling any of the Shares under this prospectus andwill not receive any of the proceeds from the sale or other disposition of the Shares by the SellingShareholder. We have agreed to pay certain registration expenses, other than commissions or discounts ofunderwriters, broker-dealers, or agents attributable to the sale of the Shares, if any. The Selling Shareholder, including its pledgees, donees, transferees, distributees, beneficiaries or othersuccessors-in-interest, may from time to time offer and sell some or all of the Shares held by them on anynational securities exchange or quotation service on which the securities maybe listed or quoted at the timeof sale, on the over-the-counter market, in one or more transactions otherwise than on these exchanges orsystems, such as privately negotiated transactions, or using a combination of these methods, and at fixedprices, at prevailing market prices at the time of the sale, at prices related to such prevailing market prices,at varying prices determined at the time of sale, or at privately negotiated prices, as described in more detailin this prospectus. Additional information on the Selling Shareholder, and the times and manner in whichthe Selling Shareholder may offer and sell or otherwise dispose of their Shares under this prospectus, isprovided under the sections titled “Selling Shareholder” and “Plan of Distribution” in this prospectus. The Selling Shareholder may sell any, all or none of the securities offered by this prospectus from timeto time and we do not know when or in what amount the Selling Shareholder may sell the Shares hereunderfollowing the effective date of the registration statement of which this prospectus forms a part. Our ordinary shares are listed on The Nasdaq Stock Market LLC under the symbol “PRQR.” OnMarch10, 2025, the last reported sale price of our ordinary shares on The Nasdaq Stock Market LLC was$1.81 per share. ProQR Therapeutics N.V. is a public company with limited liability (naamloze vennootschap)incorporated under the laws of the Netherlands. Our principal executive offices are located at Zernikedreef9, 2333 CK Leiden, The Netherlands. Our telephone number at such address is +31 88 166 7000. Investing in our securities involves a high degree of risk. See the section titled “Risk Factors” beginning onpage11of this prospectus as well as those contained in the applicable prospectus supplement and any relatedfree writing prospectus, and in the other documents that are incorporated by reference into this prospectus orthe applicable prospectus supplement. Neither the Securities and Exchange Commission nor any state or other securities commission hasapproved or disapproved of these securities or determined if this prospectus is truthful or complete. Anyrepresentation to the contrary is a criminal offense. The date of this prospectus is March25, 2025. TABLE OF CONTENTS PageABOUT THIS PROSPECTUS1CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS3PROSPECTUS SUMMARY5THE OFFERING9RISK FACTORS11CAPITALIZATION14USE OF PROCEEDS15DESCRIPTION OF SHARE CAPITAL16SELLING SHAREHOLDER37PLAN OF DISTRIBUTION41LEGAL MATTERS44EXPERTS44SERVICE OF PROCESS AND ENFORCEMENT OF LIABILITIES45EXPENSES46INCORPORATION OF CERTAIN INFORMATION BY REFERENCE47WHERE YOU CAN FIND ADDITIONAL INFORMATION48 ABOUT THIS PROSPECTUS This prospectus is part of a registration statement on Form F-3 that we filed with the Securities andExchange Commission (the “SEC”) utilizing a “shelf” registration process. Under this shelf registrationprocess, the Selling Shareholder may, at any time and from time to time, sell the securities as described inthis prospectus in one or more offerings. This prospectus does not contain all of the information set forth inthe registration statement, certain parts of which are omitted in accordance with the rules and regulations ofthe SEC. Accordingly, you should refer to the registration statement and its exhibits for further informationabout us and our securities. Copies of the regist