PROQR THERAPEUTICS N.V. Index to Unaudited Condensed Consolidated Financial Statements PAGE Unaudited Condensed Consolidated Statement of Financial Position at

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PROQR THERAPEUTICS N.V.

Index to Unaudited Condensed Consolidated Financial Statements

Unaudited Condensed Consolidated Financial Statements

PROQR THERAPEUTICS N.V.

Unaudited Condensed Consolidated Statement of Financial Position

The accompanying notes are an integral part of these unaudited interim condensed consolidated financial statements.

Unaudited Condensed Consolidated Financial Statements

PROQR THERAPEUTICS N.V.

Unaudited Condensed Consolidated Statement of Profit or Loss and OCI

( in thousands, except share and per share data)

The accompanying notes are an integral part of these unaudited interim condensed consolidated financial statements.

Unaudited Condensed Consolidated Financial Statements

PROQR THERAPEUTICS N.V.

Unaudited Condensed Consolidated Statement of Changes in Equity

The accompanying notes are an integral part of these unaudited interim condensed consolidated financial statements.

Unaudited Condensed Consolidated Financial Statements

PROQR THERAPEUTICS N.V.

Unaudited Condensed Consolidated Statement of Cash Flows

The accompanying notes are an integral part of these unaudited interim condensed consolidated financial statements.

Unaudited Condensed Consolidated Financial Statements

PROQR THERAPEUTICS N.V.

Notes to Unaudited Condensed Consolidated Financial Statements

1. General Information

ProQR Therapeutics N.V., or "ProQR" or the "Company", is a biotechnology company domiciled in the Netherlands that primarily focuses on the discovery and development of novel therapeutic medicines.

Since September 18, 2014, the Company's ordinary shares have been listed on Nasdaq. They are currently trading at Nasdaq Capital Market under ticker symbol PRQR.

The Company was incorporated in the Netherlands, on February 21, 2012 (Chamber of Commerce no. 54600790) and was reorganized from a private company with limited liability to a public company with limited liability on September 23, 2014. The Company has its statutory seat in Leiden, the Netherlands. The address of its headquarters and registered office is Zernikedreef 9, 2333 CK Leiden, the Netherlands.

ProQR Therapeutics N.V. is the ultimate parent company of the following entities:

ProQR Therapeutics N.V. is also statutory director of Stichting Bewaarneming Aandelen ProQR ("ESOP Foundation") and has full control over this entity.

As used in these condensed consolidated financial statements, unless the context indicates otherwise, all references to "ProQR" or the "Company" refer to ProQR Therapeutics N.V. including its subsidiaries and the ESOP Foundation.

Unaudited Condensed Consolidated Financial Statements

2. Significant Accounting Policies

These interim condensed consolidated financial statements for the three and nine month periods ended September 30, 2024 have been prepared in accordance with IAS 34 Interim Financial Statements. They should be read in conjunction with the Company's annual financial statements for the year ended December 31, 2023. These interim condensed consolidated financial statements do not include all information required for a complete set of financial statements prepared in accordance with IFRS Standards. However, selected explanatory notes are included to explain events and transactions that are significant to an understanding of the changes in the Company's financial position and performance since the last annual financial statements. In the opinion of management, all events and transactions that are significant to an understanding of the changes in financial position and performance of the Company since the end of the last annual reporting period are disclosed in these interim condensed consolidated financial statements. The accounting policies adopted in the preparation of the interim condensed consolidated financial statements are consistent with those applied in the preparation of the Company's annual financial statements for the year ended December 31, 2023.

During the nine month period ended September 30, 2024, the Company invested in financial assets in the form of deposits with an original maturity of longer than three months but shorter than twelve months as described in Note 6. Financial assets are measured at amortized cost as they give rise on specified dates to cash flows that are solely payments of principal and interest on the principal amount outstanding.

The Company's financial results have varied substantially, and are expected to continue to vary, from period to period. The Company believes that its ordinary activities are not linked to any particular seasonal factors.

The management of ProQR has, upon preparing and finalizing these interim condensed consolidated financial statements, assessed the Company's ability to fund its operations for a period of at least one year after the date of signing these interim condensed consolidated financial statements. Management expects the Company to continue as a going concern based on its existing funding, taking into account the Company's current cash position and the projected cash flows based on the activities under execution on the basis of ProQR's business plan and budget. Thus, we continue to adopt the going concern basis of accounting in preparing the interim condensed consolidated financial statements.

The carrying amount of all financial assets and financial liabilities is a reasonable approximation of the fair value and therefore, information about the fair values of each class has not been disclosed.

The Company operates in one reportable segment, which comprises the discovery and development of innovative, RNA based therapeutics.

3. Adoption of New and Revised International Financial Reporting Standards

New Standards and Interpretations, which became effective as of January 1, 2024, did not have a material impact on our condensed consolidated financial statements.

Unaudited Condensed Consolidated Financial Statements

4. Critical Accounting Estimates and Judgments

In the application of the Company's accounting policies, management is required to make judgments, estimates and assumptions about the carrying amounts of assets and liabilities that are not readily apparent from other sources. The estimates and associated assumptions are based on historical experience and other factors that are considered to be relevant. Actual results may differ from these estimates.

The estimates and underlying assumptions are reviewed on an ongoing basis. Revisions to accounting estimates are recognized in the period in which the estimate is revised if the revision affects only that period or in the period of the revision and future periods if the revision affects both current and future periods.

The significant judgements made by management in applying the Company's accounting policies, except for the significant judgements related to revenue recognition from milestone payments as further described below and in Note 14, and the key sources of estimation uncertainty were the same as those described in the Company's annual financial statements for the year ended December 31, 2023.

Revenue recognition for the Eli Lilly collaboration and license agreement

a. Identification of the performance obligation

Note 14 describes the Company's original research and collaboration agreement with Eli Lilly and Company, and the amended and restated research and collaboration agreement (collectively, the "Collaboration agreement"). Under the Collaboration agreement, ProQR provides Eli Lilly with a license (with a right to sub-license) to exploit compounds resulting from the collaboration. A significant amount of judgement is required to determine whether the license is distinct from the other promises in the contract. The license was concluded not to be distinct from the other promises in the contract based on the following considerations:

ProQR's services are evaluated as predominant at inception of the contract and contractually only ProQR can perform these services as they are specific to the skills of the Company. The resulting compounds from the collaboration do not represent a series of distinct promises because they were not predetermined at the inception of the contract and can be terminated or replaced at the discretion of Lilly subject to the terms and conditions of the Collaboration agreement.

b. Determining the timing of satisfaction of performance obligations

Under the Collaboration agreement, the Company recognizes revenue over time, using an input method that estimates the satisfaction of the performance obligation as the percentage of labor hours incurred compared to the total estimated labor hours required to complete the promised services. As our estimate of the total labor hours required is dependent on the evolution of the research and development activities, it may be subject to change. If the progression and/or outcome of certain research and development activities would be different from the assumptions that were made during the preparation of these financial statements, this could lead to material adjustments to the total estimated labor hours, which might result in a reallocation of revenue between current and future periods. Our total deferred revenue balance amounts to 55,588,000 of which 55,236,000 is related to this Eli Lilly performance obligation at September 30, 2024. As at December 31, 2023 the entire deferred revenue balance of 64,739,000 related to the Eli Lilly performance obligation.

Unaudited Condensed Consolidated Financial Statements

c. Determining the transaction price

The Company applied judgement to determine whether the equity investments made by Eli Lilly in ProQR are part of the transaction price for the Collaboration agreement. The Company concluded that the differences between the prices that Eli Lilly paid for the shares and the ProQR stock closing prices on the days of entering into the equity investment agreements arose because of the Company's existing obligations to deliver research and development services to Eli Lilly under the terms of the Collaboration agreement. Therefore, the above differences between the closing share prices on the agreement effective dates and the equity investment prices paid by Eli Lilly are considered to be part of the transaction price of the contract and are initially allocated to deferred revenue.

The contract also includes variable consideration, but no variable consideration was included in the initial transaction price at the inception, as it is not highly probable that a significant reversal in the amount of cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. The Company includes such variable consideration in the transaction price when the uncertainty associated with the variable consideration is resolved.

As further described in Note 14, during 2024, the Company reached milestones under the agreement, which were added to the transaction price and recognized partially as revenue during 2024 with the remainder recorded in future periods based on progress towards satisfaction of performance obligation.

The Collaboration agreement includes sales-based royalties, including commercial milestone payments based on the level of sales. Related revenue is recognized as the subsequent underlying sales occur at a point in time.

Research and development expenditures

Research expenditures are reflected in the income statement. Development expenses are currently also reflected in the income statement because the criteria for capitalization are not met. At each balance sheet date, the Company estimates the level of service performed by the vendors and the associated costs incurred for the services performed.

Although we do not expect the estimates to be materially different from amounts actually incurred, the understanding of the status and timing of services performed relative to the actual status and timing of services performed may vary and could result in reporting amounts that are too high or too low in any particular period.

5. Cash and Cash Equivalents

At September 30, 2024, the Company's cash and cash equivalents were 89,401,000 compared to 118,925,000 at December 31, 2023. The cash balances are held at banks with investment grade credit ratings. Short-term credit ratings must be rated A-1/P-1/F1 at a minimum by at least one of the Nationally Recognized Statistical Rating Organizations ("NRSROs") specifically Moody's, Standard & Poor's or Fitch. The cash at banks is at full disposal of the Company. Included in cash and cash equivalents are deposits fixed for at most 3-month periods at a time.

6. Financial Asset - Current

During the nine month period ended September 30, 2024, the Company placed a term deposit with an initial maturity longer than 3 months but less than 12 months. This deposit did not qualify as a cash equivalent. The deposit was held at a bank with an investment grade credit rating. Short-term credit ratings must be rated A-1/P-1/F1 at a minimum by at least one of the NRSROs specifically Moody's, Standard & Poor's or Fitch. The deposit was repaid as of September 30, 2024.

Unaudited Condensed Consolidated Financial Statements

7. Prepayments and Other Receivables

At September 30, 2024 and December 31, 2023 prepayments consisted principally of payments made by the Company for services not yet provided by vendors. At September 30, 2024 and December 31, 2023 other receivables consisted principally of amounts receivable from research collaboration partners and deposits.

8. Property, Plant and Equipment

At September 30, 2024 and December 31, 2023, property plant and equipment consisted of buildings and leasehold improvements, laboratory equipment and other assets. Buildings and leasehold improvements include a right-of-use asset relating to the lease of our Leiden office and laboratory space, with a carrying amount of 11,873,000 at September 30, 2024 (December 31, 2023: 14,524,000).

9. Other Current Liabilities

At September 30, 2024, other current liabilities amount to 7,439,000 (December 31, 2023: 8,509,000). At September 30, 2024 and December 31, 2023, other current liabilities consisted principally of accruals for services provided by vendors not yet billed, payroll related accruals and other miscellaneous liabilities.

On December 10, 2018 ProQR was awarded an Innovation credit for the sepofarsen program. Amounts were drawn under this facility from 2018 through 2022. The credit of 3,907,000 was used to conduct the Phase 2/3 clinical study and efforts to obtain regulatory and ethical market approval (New Drug Applications ("NDA")/ Marketing Authorization Applications ("MAA")) of sepofarsen for LCA10. In 2023, ProQR made a partial repayment of the principal, amounting to 1,008,000. The remaining amount payable of 2,899,000 and accrued interest is recognized under current borrowings at September 30, 2024 and non-current borrowings at December 31, 2023.

In December 2023, ProQR received a conditional waiver of the balance of the Innovation credit including accrued interest. Consequently, the repayment of the total loan of 4,510,000, including interest, will be waived if conditions are met, which will be reviewed annually.

Unaudited Condensed Consolidated Financial Statements

In September 2022, ProQR extinguished its debt with Pontifax and Kreos by repaying all outstanding principal amounts. Pontifax' and Kreos' warrants remain in place until their five-year economic life expires in 2025 and 2026. These warrants are accounted for as embedded derivatives and were recognized separately from the host contract as derivative financial liabilities at fair value through profit or loss.

11. Lease Liabilities

At September 30, 2024 and December 31, 2023, lease liabilities primarily consisted of the Company's lease of office and laboratory facilities at Zernikedreef in Leiden, the Netherlands.

The Company leases office and laboratory facilities of 4,818 square meters at Zernikedreef in Leiden, the Netherlands, where our headquarters and our laboratories are located. The current lease agreement for these facilities terminates on September 30, 2031. The lease agreement contains no significant dismantling requirements.

The initial 10-year lease agreement for the Leiden office and laboratory facilities was accounted for as of commencement date July 1, 2020. This 10-year period was extended by 1 year to an 11-year period in December 2020. The lease contract may be extended for subsequent 5-year periods. As the Company is not reasonably certain to exercise these extension options, these are not included in the lease term.

The carrying amount of the right-of-use asset is disclosed in Note 8.

The following table summarizes details of deferred income at September 30, 2024 and December 31, 2023. The nature of the deferred income is described in Note 14 and 15.

Unaudited Condensed Consolidated Financial Statements

13. Shareholders' Equity

The authorized share capital of the Company amounting to 13,600,000 consists of 170,000,000 ordinary shares and 170,000,000 preference shares with a par value of 0.04 per share. At September 30, 2024, 84,247,306 ordinary shares were issued. 81,683,382 ordinary shares were fully paid and 2,563,924 ordinary shares were held by the Company as treasury shares (December 31, 2023: 2,893,792).

On September 30, 2024, the Company filed a shelf registration statement on Form F-3, which permitted the offering, issuance and sale by the Company of up to a maximum aggregate offering price of $ 300,000,000 of its ordinary shares, warrants and/or units. In relation to this registration statement, on September 30, 2024, the Company entered into a sales agreement with Cantor Fitzgerald & Co, which permitted the offering, issuance and sale by the Company of up to a maximum aggregate offering price of $ 75,000,000 of its ordinary shares that may be issued and sold in one or more at-the-market ("ATM') offerings. The company will pay Cantor Fitzgerald & Co a commission equal to 3% of the gross proceeds of the sales price of all ordinary shares sold through it as sales agent under the sale agreement. The Company defers direct, incremental costs associated to this offering, except for the commission costs to Cantor Fitzgerald & Co, which are a reduction to additional paid-in capital, and will deduct these costs from additional paid-in capital in the consolidated balance sheet proportionately to the amount of proceeds raised. In 2024, no shares were issued pursuant to this ATM facility through September 30, 2024. Refer to Note 22, for explanation of events occurring after the reporting date.

The translation reserve comprises all foreign currency differences arising from the translation of the financial statements of foreign operations.

The Company operates an equity-settled share-based compensation plan, which was introduced in 2013. Options and Restricted Stock Units ("RSUs") may be granted to employees, members of the Supervisory Board, members of the Management Board and consultants. The compensation expenses included in operating costs for this plan in the nine month period ended September 30, 2024 were 1,976,000 (nine month period ended September 30, 2023: 2,304,000), of which 1,559,000 was recorded in general and administrative costs (nine month period ended September 30, 2023: 2,010,000) and 417,000 was recorded in research and development costs (nine month period ended September 30, 2023: 294,000).

In September 2021, the Company entered into a global licensing and research collaboration with Eli Lilly and Company ("Lilly") focused on the discovery, development, and commercialization of potential new medicines for genetic disorders in the liver and nervous system. ProQR and Lilly will use ProQR's proprietary Axiomer RNA editing platform to progress new drug targets toward clinical development and commercialization.

Under the terms of the agreement, ProQR received an upfront payment and equity consideration, and is eligible to receive milestone payments and royalties on the net sales of any resulting products. In September 2021, the Company issued 3,989,976 shares to Lilly, resulting in net proceeds of $30,000,000 ( 25,270,000). This amount included a price premium of $2,429,000 ( 2,047,000), which was determined to be part of the transaction price and as such was initially recognized as deferred revenue. An up-front payment of $20,000,000 ( 16,849,000) was received in October 2021.

Unaudited Condensed Consolidated Financial Statements

With regard to its original collaboration with Lilly, the Company concluded as follows:

In December 2022, the Company and Lilly amended their research and collaboration agreement described above, which expanded the collaboration. Under the amended and restated research and collaboration agreement, Lilly will gain access to additional targets in the central nervous system and peripheral nervous system with ProQR's Axiomer platform.