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IONIS PHARMACEUTICALS INC

For the period ended Jun 30, 2024. Filed Aug 1, 2024.

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About this filing

A company's report for each of its first three quarters. The financial statements are not audited. It shows how the business has moved since the last annual report, and what management says changed.

Jun 30, 2024 · Filed Aug 1, 2024

IONS$39.42+1.6%Stored close · as of Nov 6, 2026

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Notes to Condensed Consolidated Financial Statements (unaudited)

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

June 30, 2024

  1. Organization and Basis of Presentation

Organization and Business Activity

We incorporated in California on January 10, 1989. In conjunction with our initial public offering, we reorganized as a Delaware corporation in April 1991. We are a leader in the discovery and development of RNA-targeted therapeutics.

Basis of Presentation

We prepared the unaudited interim condensed consolidated financial statements for the three and six months ended June 30, 2024 and 2023 on the same basis as the audited financial statements for the year ended December 31, 2023. We included all normal recurring adjustments in the financial statements, which we considered necessary for a fair presentation of our financial position at such dates and our operating results and cash flows for those periods. Our operating results for the interim periods may not be indicative of what our operating results will be for the entire year. For more complete financial information, these financial statements, and notes thereto, should be read in conjunction with the audited financial statements for the year ended December 31, 2023 included in our Annual Report on Form 10-K filed with the Securities and Exchange Commission, or SEC.

In our condensed consolidated financial statements, we included the accounts of Ionis Pharmaceuticals, Inc. and the consolidated results of our wholly owned subsidiary, Akcea Therapeutics, Inc. and its wholly owned subsidiaries (“we”, “us” or “our”).

We operate as asingle segment, Ionis operations, because our chief decision maker reviews operating results on an aggregate basis and manages our operations as asingle operating segment.

Use of Estimates

We prepare our condensed consolidated financial statements in conformity with accounting principles generally accepted in the United States, or U.S., that require us to make estimates and assumptions that affect the amounts reported in our condensed consolidated financial statements and accompanying notes. Actual results could differ from our estimates.

  1. Significant Accounting Policies

Our significant accounting policies have not changed substantially from those included in our Annual Report on Form 10-K for the year ended December 31, 2023.

Recently Issued Accounting Standards

We do not expect any recently issued accounting standards to have a material impact to our financial results.

  1. Supplemental Financial Data

Inventories

Our inventory consisted of the following (in thousands):

June 30, 2024December 31, 2023
Raw materials:
Raw materials - clinical$22,211$20,985
Raw materials - commercial2,4121,809
Total raw materials24,62322,794
Work in process3,6145,477
Finished goods486154
Total inventories$28,723$28,425

Index

Accrued Liabilities

Our accrued liabilities consisted of the following (in thousands):

June 30, 2024December 31, 2023
Clinical development expenses$82,017$105,967
In-licensing expenses10,6037,454
Commercial expenses4,5834,875
Other miscellaneous expenses17,12729,598
Total accrued liabilities$114,330$147,894
  1. Revenues

During the three and six months ended June 30, 2024 and 2023, our revenues were comprised of the following (in thousands):

Three Months Ended June 30,Six Months Ended June 30,
2024202320242023
Revenue:
Commercial revenue:
SPINRAZA royalties$56,743$61,012$95,198$111,258
WAINUA royalties3,781—4,907—
Other commercial revenue:
TEGSEDI and WAYLIVRA revenue, net8,19210,65516,82017,133
Licensing and other royalty revenue3,3206,23014,70417,273
Total other commercial revenue11,51216,88531,52434,406
Total commercial revenue72,03677,897131,629145,664
Research and development revenue:
Collaborative agreement revenue141,52491,013190,870129,347
WAINUA joint development revenue11,69019,50122,24943,924
Total research and development revenue153,214110,514213,119173,271
Total revenue$225,250$188,411$344,748$318,935

Revenue Sources

The following are sources of revenue and when we typically recognize revenue.

Commercial Revenue: SPINRAZA royalties and WAINUA royalties

We earn commercial revenue primarily in the form of royalty payments on net sales of SPINRAZA. In 2024, we began earning royalties from WAINUA sales.

Commercial Revenue: TEGSEDI and WAYLIVRA revenue, net

We earn commercial revenue from TEGSEDI and WAYLIVRA sales under our distribution agreements with Sobi. In addition, we receive royalties from PTC Therapeutics International Limited, or PTC, for TEGSEDI and WAYLIVRA sales.

Commercial Revenue: Licensing and other royalty revenue

We also recognize as commercial revenue sales milestone payments and royalties we earn under our partnerships. For example, we earn royalty revenue on net sales of QALSODY, which is included in Licensing and other royalty revenue.

Research and development revenue under collaboration agreements

We enter into collaboration agreements to license and sell our technology on an exclusive or non-exclusive basis. Our collaboration agreements typically contain multiple elements, or performance obligations, including technology licenses or options to obtain technology licenses, research and development, or R&D, services and manufacturing services.

Index

Upfront payments: When we enter into a collaboration agreement and receive an upfront payment, we typically record the entire upfront payment as deferred revenue if our only performance obligation is for R&D services we will provide in the future. We amortize the upfront payment into revenue as we perform the R&D services. If part or all of the upfront payment is a license fee, we recognize as revenue the portion related to the license when we deliver the license to our partner because our partner has full use of the license and we do not have any additional performance obligations related to the license after delivery.

Milestone payments: We include variable consideration in the transaction price when it is probable. We typically include milestone payments for R&D services in the transaction price when they are achieved. We include these milestone payments when they are achieved because typically there is considerable uncertainty in the R&D processes that trigger these payments. Similarly, we include approval milestone payments in the transaction price once the medicine is approved by the applicable regulatory agency. We will recognize sales-based milestone payments in the period in which we achieve the milestone under the sales-based royalty exception allowed under accounting rules.

We recognize milestone payments that relate to an ongoing performance obligation over our period of performance. For example, when we achieve a milestone payment from a partner for advancing a clinical study under a collaboration agreement, we add the milestone payment to the transaction price if the milestone relates to an ongoing R&D services performance obligation and recognize revenue related to the milestone payment over our estimated period of performance. If we have partially completed our performance obligation, then we record a cumulative-effect adjustment in the period we add the milestone payment to the transaction price.

Conversely, we recognize in full those milestone payments that we earn based on our partners’ activities when our partner achieves the milestone event and we do not have a performance obligation.

License fees: We recognize as revenue the total amount we determine to be the relative stand-alone selling price of a license when we deliver the license to our partner because our partner has full use of the license and we do not have any additional performance obligations related to the license after delivery.

WAINUA (Eplontersen) Collaboration with AstraZeneca

In 2021, we entered into a joint development and commercialization agreement with AstraZeneca to develop and commercialize WAINUA for the treatment of transthyretin amyloidosis, or ATTR. We jointly developed and are commercializing WAINUA with AstraZeneca in the U.S. for the treatment of adults with polyneuropathy caused by hereditary ATTR, or ATTRv-PN. We initially granted AstraZeneca exclusive rights to commercialize WAINUA outside the U.S., except for certain Latin American countries. In 2023, we expanded those rights to include Latin America. Under the terms of the agreement, we received a $200 million upfront payment in 2021.

We evaluated our WAINUA collaboration under ASC 808 and identified four material components: (i) the license we granted to AstraZeneca in 2021, (ii) the co-development activities that we and AstraZeneca are performing, (iii) the co-commercialization activities that we and AstraZeneca are performing and (iv) the co-medical affairs activities that we and AstraZeneca are performing.

We determined that we had a vendor-customer relationship within the scope of Accounting Standards Codification, or ASC, Topic 606, Revenue from Contracts with Customers, or ASC 606, for the license we granted to AstraZeneca and as a result we hadone performance obligation. For our sole performance obligation, we determined the transaction price was the $200 million upfront payment we received. We recognized the upfront payment in full in 2021 because we did not have any remaining performance obligations after we delivered the license to AstraZeneca.

We also concluded that the co-development activities, the co-commercialization activities and the co-medical affairs activities are within the scope of ASC Topic 808, Collaborative Arrangements, or ASC 808, because we and AstraZeneca are active participants exposed to the risks and benefits of the activities under the collaboration and therefore do not have a vendor-customer relationship. AstraZeneca is currently responsible for 55 percent of the costs associated with the ongoing global Phase 3 development program. Because we are leading the Phase 3 development program, we made an accounting policy election to recognize as non-customer revenue the cost-share funding from AstraZeneca, net of our share of AstraZeneca’s development expenses, in the same period we incur the related development expenses. As AstraZeneca is responsible for the majority of the commercial and medical affairs costs in the U.S. and all costs associated with bringing WAINUA to market outside the U.S., we made an accounting policy election to recognize cost-share funding we receive from AstraZeneca related to commercial and medical affairs activities as reductions of our selling, general and administrative, or SG&A, expense and R&D expense, respectively.

Index

  1. Collaborative Arrangements and Licensing Agreements

Below, we have included our AstraZeneca, Biogen, Otsuka and Roche collaborations, which are the collaborations with substantive changes during 2024 from those included in Part IV, Item 15, Note 4, Collaborative Arrangements and Licensing Agreements, of our audited financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2023.

AstraZeneca

We havetwo collaborations with AstraZeneca, one focused on the joint development and commercialization of WAINUA andone focused on the treatment of cardiovascular, renal and metabolic diseases. From inception through June 30, 2024, we have received more than $920 million from these collaborations.

Over the term of our WAINUA collaboration, we are eligible to receive up to $3.6 billion, which is comprised of a $200 million upfront payment, up to $485 million in development and approval milestone payments and up to $2.9 billion in sales milestone payments. The agreement includes territory-specific development, commercial and medical affairs cost-sharing provisions. In addition, we are eligible to receive up to mid-20 percent royalties for sales in the U.S. and tiered royalties up to the high teens for sales outside the U.S.

In January 2024, we and AstraZeneca launched WAINUA in the U.S. for the treatment of adults with ATTRv-PN. As a result, we began earning royalties from WAINUA sales, which we recognize as commercial revenue in our condensed consolidated statements of operations. We will achieve the next payment of up to $30 million upon regulatory approval of WAINUA for ATTRv-PN in the European Union, or EU, under this collaboration.

During the three and six months ended June 30, 2024 and 2023, we earned the following revenue from our relationship with AstraZeneca (in thousands, except percentage amounts):

Three Months Ended June 30,Six Months Ended June 30,
2024202320242023
Revenue from our relationship with AstraZeneca$15,960$59,501$27,645$83,926
Percentage of total revenue7%32%8%26%

Our condensed consolidated balance sheet at June 30, 2024 included deferred contract revenue of $1.9 million from our relationship with AstraZeneca. We didnot have any deferred contract revenue from our relationship with AstraZeneca at December 31, 2023.

Biogen

We have several strategic collaborations with Biogen focused on using antisense technology to advance the treatment of neurological disorders. We developed and licensed to Biogen SPINRAZA, our approved medicine to treat people with spinal muscular atrophy, or SMA. QALSODY, our medicine to treat patients with superoxide dismutase 1 amyotrophic lateral sclerosis, or SOD1-ALS, received accelerated approval from the U.S. Food and Drug Administration, or FDA, in April 2023 and marketing authorization under exceptional circumstances from the European Medicines Agency, or EMA, in May 2024. In addition, we and Biogen are currently developing numerous other investigational medicines to treat neurodegenerative diseases, including medicines in development to treat people with amyotrophic lateral sclerosis, or ALS, SMA, Alzheimer’s disease, or AD, and Parkinson’s disease, or PD. In addition to these medicines, our collaborations with Biogen include a substantial research pipeline that addresses a broad range of neurological diseases. From inception through June 30, 2024, we have received more than $3.9 billion in payments from our Biogen collaborations, including payments to purchase our stock.

Under our 2013 strategic neurology collaboration, we earned a $20 million milestone payment from Biogen when the EMA approved Biogen’s Marketing Authorization Application, or MAA, filing of QALSODY in the second quarter of 2024. We recognized this milestone payment as R&D revenue in full in the second quarter of 2024 because we did not have any remaining performance obligations related to the milestone payment. We will achieve the next milestone payment for QALSODY of $10 million if the Ministry of Health, Labour and Welfare of Japan approves Biogen’s Japanese New Drug Application filing of QALSODY.

In the second quarter of 2024, Biogen's option to license ION582, an investigational antisense medicine for the potential treatment of Angelman Syndrome, expired unexercised. As a result, we recognized $30 million of R&D revenue from previously deferred milestone payments related to the ION582 study because we did not have any remaining performance obligations. We will achieve the next milestone payment of $25 million if Biogen advances IONIS-MAPTRx into Phase 3 development under our 2012 neurology collaboration.

Index

During the three and six months ended June 30, 2024 and 2023, we earned the following revenue from our relationship with Biogen (in thousands, except percentage amounts):

Three Months Ended June 30,Six Months Ended June 30,
2024202320242023
Revenue from our relationship with Biogen$138,159$97,402$197,395$167,903
Percentage of total revenue61%52%57%53%

Our condensed consolidated balance sheets at June 30, 2024 and December 31, 2023 included deferred contract revenue of $241.8 million and $307.4 million, respectively, from our relationship with Biogen.

Otsuka

In 2023, we entered into an agreement with Otsuka Pharmaceutical Co., Ltd., or Otsuka, to commercialize donidalorsen in Europe. In the second quarter of 2024, we expanded the agreement to include commercialization rights for donidalorsen in the Asia-Pacific region in addition to Europe. As a result, we received a $20 million upfront payment from Otsuka. Under the amended agreement, we are eligible to receive up to $290 million, which is comprised of $85 million in upfront payments, up to $65 million in regulatory milestone payments and up to $140 million in sales milestone payments over the term of the collaboration. In addition, we are eligible to receive tiered royalties up to 30 percent on net sales. We are responsible for completing the ongoing development of donidalorsen. We retained the rights to commercialize donidalorsen in the U.S. and in the rest of the world, assuming regulatory approvals. From inception through June 30, 2024, we have received $85 million in payments from Otsuka.

We identifiedtwo performance obligations under our amended agreement for the Asia-Pacific region, comprised of our license of donidalorsen to Otsuka and R&D services for donidalorsen. We allocated the transaction price of $20 million based on the estimated stand-alone selling price of each performance obligation as follows:

●$17.5 million for the license of donidalorsen; and
●$2.5 million for the R&D services for donidalorsen.

In the second quarter of 2024, we recognized $17.5 million as revenue in full because Otsuka had full use of the license without any continuing involvement from us. We are recognizing revenue for our R&D services performance obligation as we perform services based on our effort to satisfy our performance obligation relative to our total effort expected to satisfy our performance obligation. We currently estimate we will satisfy our R&D services performance obligation in March 2026. We will achieve the next payment of $15 million if the EMA accepts a MAA filing for donidalorsen in the EU under this collaboration.

During the three and six months ended June 30, 2024 and 2023, we earned the following revenue from our relationship with Otsuka (in thousands, except percentage amounts):

Three Months Ended June 30,Six Months Ended June 30,
2024202320242023
Revenue from our relationship with Otsuka$18,905$—$19,691$—
Percentage of total revenue8%0%6%0%

Our condensed consolidated balance sheets at June 30, 2024 and December 31, 2023 included deferred contract revenue of $8.8 million and $8.5 million, respectively, from our relationship with Otsuka.

Roche

We have three collaborations with Hoffmann-La Roche Inc. and F. Hoffmann-La Roche Ltd, collectively Roche: one todevelop treatments for Huntington’s disease, or HD, one to develop IONIS-FB-LRx for the treatment of immunoglobulin A, or IgA, nephropathy, or IgAN, andone to develop RNA-targeted programs for AD and HD. From inception through June 30, 2024, we have received more than $345 million in payments from our Roche collaborations.

In July 2024, Roche discontinued development of IONIS-FB-LRx for the treatment of geographic atrophy, or GA, following the completion of the Phase 2 study, which showed a favorable safety profile and target engagement, but insufficient efficacy to advance into Phase 3 development.

Index

Over the term of the IONIS-FB-LRx collaboration for the treatment of IgAN, we are eligible to receive up to $430 million, which is comprised of a $35 million license fee, up to $25 million in development milestone payments, up to $90 million in regulatory milestone payments and up to $280 million in sales milestone payments. We will achieve the next payment of $23.5 million if Roche advances IONIS-FB-LRx for the treatment of IgAN under this collaboration.

During the three and six months ended June 30, 2024 and 2023, we earned the following revenue from our relationship with Roche (in thousands, except percentage amounts):

Three Months Ended June 30,Six Months Ended June 30,
2024202320242023
Revenue from our relationship with Roche$11,089$5,754$22,595$8,121
Percentage of total revenue5%3%7%3%

Our condensed consolidated balance sheets at June 30, 2024 and December 31, 2023 included deferred contract revenue of $15.0 million and $36.7 million, respectively, from our relationship with Roche.

  1. Basic and Diluted Net Loss Per Share

Basic net loss per share

We calculated our basic net loss per share for the three and six months ended June 30, 2024 and 2023 by dividing our net loss by our weighted-average number of common shares outstanding during the period.

Diluted net loss per share

For the three and six months ended June 30, 2024 and 2023, we incurred a net loss; therefore, we did not include dilutive common equivalent shares in the computation of diluted net loss per share because the effect would have been anti-dilutive. Common stock from the following would have had an anti-dilutive effect on net loss per share:

●1.75 percent convertible senior notes, or 1.75% Notes;
●0 percent convertible senior notes, or 0% Notes;
●Note hedges related to the 0% Notes;
●0.125 percent convertible senior notes, or 0.125% Notes;
●Note hedges related to the 0.125% Notes;
●Dilutive stock options;
●Unvested restricted stock units, or RSUs;
●Unvested performance restricted stock units, or PRSUs; and
●Employee Stock Purchase Plan, or ESPP.

Additionally, as of June 30, 2024 and 2023, we had warrants related to our 0% and 0.125% Notes outstanding. We will include the shares issuable under these warrants in our calculation of diluted earnings per share when the average market price per share of our common stock for the reporting period exceeds the strike price of the warrants.

  1. Investments

The following table summarizes the contract maturity of the available-for-sale securities we held as of June 30, 2024:

One year or less75%
After one year but within two years21%
After two years but within three and a half years4%
Total100%

As illustrated above, at June 30, 2024,96 percent of our available-for-sale securities had a maturity of less thantwo years.

All of our available-for-sale debt securities are available to us for use in our current operations. As a result, we categorize all of these securities as current assets even though the stated maturity of some individual securities may be one year or more beyond the balance sheet date.

We invest in debt securities with strong credit ratings and an investment grade rating at or above A-1, P-1 or F-1 by Standard & Poor’s, Moody’s or Fitch, respectively.

At June 30, 2024, we had an equity ownership interest of less than 20 percent inseven private companies andthree public companies with which we conduct business.

Index

The following is a summary of our investments (in thousands):

Amortized · Gross Unrealized · Estimated
June 30, 2024CostGainsLossesFair Value
Available-for-sale debt securities:
Corporate debt securities (1)$552,837$36$(1,569)$551,304
Debt securities issued by U.S. government agencies121,7815(310)121,476
Debt securities issued by the U.S. Treasury (1)650,99712(1,105)649,904
Debt securities issued by states of the U.S. and political subdivisions of the states18,08314(42)18,055
Total debt securities with a maturity of one year or less1,343,69867(3,026)1,340,739
Corporate debt securities218,639191(874)217,956
Debt securities issued by U.S. government agencies115,34972(317)115,104
Debt securities issued by the U.S. Treasury127,24012(1,135)126,117
Debt securities issued by states of the U.S. and political subdivisions of the states1,668—(8)1,660
Total debt securities with a maturity of more than one year462,896275(2,334)460,837
Total available-for-sale debt securities$1,806,594$342$(5,360)$1,801,576
Equity securities:
Publicly traded equity securities included in other current assets (2)$11,897$334$(5,377)$6,854
Privately held equity securities included in deposits and other assets (3)23,11525,001(7,093)41,023
Total equity securities35,01225,335(12,470)47,877
Total available-for-sale debt and equity securities$1,841,606$25,677$(17,830)$1,849,453
Amortized · Gross Unrealized · Estimated
December 31, 2023CostGainsLossesFair Value
Available-for-sale debt securities:
Corporate debt securities (1)$559,967$157$(2,625)$557,499
Debt securities issued by U.S. government agencies224,71164(611)224,164
Debt securities issued by the U.S. Treasury (1)513,784152(1,889)512,047
Debt securities issued by states of the U.S. and political subdivisions of the states17,75742(113)17,686
Total debt securities with a maturity of one year or less1,316,219415(5,238)1,311,396
Corporate debt securities243,1511,270(692)243,729
Debt securities issued by U.S. government agencies110,138547(21)110,664
Debt securities issued by the U.S. Treasury294,8731,239(480)295,632
Debt securities issued by states of the U.S. and political subdivisions of the states3,4667(4)3,469
Total debt securities with a maturity of more than one year651,6283,063(1,197)653,494
Total available-for-sale debt securities$1,967,847$3,478$(6,435)$1,964,890
Equity securities:
Publicly traded equity securities included in other current assets (2)$11,897$236$(5,832)$6,301
Privately held equity securities included in deposits and other assets (3)23,11525,001(5,125)42,991
Total equity securities35,01225,237(10,957)49,292
Total available-for-sale debt and equity securities$2,002,859$28,715$(17,392)$2,014,182
(1)Includes investments classified as cash equivalents in our condensed consolidated balance sheets.
(2)Our publicly traded equity securities are included in other current assets. We recognize publicly traded equity securities at fair value. In the six months ended June 30, 2024, we recorded a $0.6 million net unrealized gain in our condensed consolidated statements of operations related to changes in the fair value of our investments in publicly traded companies.
(3)Our privately held equity securities are included in deposits and other assets. We recognize our privately held equity securities at cost minus impairments, plus or minus changes resulting from observable price changes in orderly transactions for the identical or similar investment of the same issuer, which are Level 3 inputs. In the six months ended June 30, 2024, we recorded a loss of $2.0 million in our condensed consolidated statements of operations related to changes in the fair value of our investments in privately held companies.

Index

The following is a summary of our investments we consider to be temporarily impaired at June 30, 2024 (in thousands, except for number of investments):

Less than 12 Months of Temporary Impairment · More than 12 Months of Temporary Impairment · Total Temporary Impairment
Number of InvestmentsEstimated Fair ValueUnrealized LossesEstimated Fair ValueUnrealized LossesEstimated Fair ValueUnrealized Losses
Corporate debt securities440$517,394$(1,155)$142,390$(1,288)$659,784$(2,443)
Debt securities issued by U.S. government agencies108173,618(482)25,892(145)199,510(627)
Debt securities issued by the U.S. Treasury71561,363(862)154,006(1,378)715,369(2,240)
Debt securities issued by states of the U.S. and political subdivisions of the states458,449(23)9,319(27)17,768(50)
Total temporarily impaired securities664$1,260,824$(2,522)$331,607$(2,838)$1,592,431$(5,360)

We believe that the decline in value of these securities is temporary and is primarily related to the change in market interest rates since purchase rather than underlying credit deterioration for any of the issuers. We believe it is more likely than not that we will be able to hold our debt securities with declines in value to maturity. Therefore, we intend to hold these securities to maturity and anticipate full recovery of our debt securities’ amortized cost basis at maturity.

  1. Fair Value Measurements

The following tables present the major security types we held at June 30, 2024 and December 31, 2023 that we regularly measure and carry at fair value. The following tables segregate each security type by the level within the fair value hierarchy of the valuation techniques we utilized to determine the respective security’s fair value (in thousands):

At June 30, 2024Quoted Prices in Active Markets (Level 1)Significant Other Observable Inputs (Level 2)
Cash equivalents (1)$212,489$212,489$—
Corporate debt securities (2)769,260—769,260
Debt securities issued by U.S. government agencies (3)236,580—236,580
Debt securities issued by the U.S. Treasury (3)776,021776,021—
Debt securities issued by states of the U.S. and political subdivisions of the states (3)19,715—19,715
Publicly traded equity securities included in other current assets (4)6,8546,854—
Total$2,020,919$995,364$1,025,555
At December 31, 2023Quoted Prices in Active Markets (Level 1)Significant Other Observable Inputs (Level 2)
Cash equivalents (1)$185,424$185,424$—
Corporate debt securities (5)801,228—801,228
Debt securities issued by U.S. government agencies (3)334,828—334,828
Debt securities issued by the U.S. Treasury (3)807,679807,679—
Debt securities issued by states of the U.S. and political subdivisions of the states (3)21,155—21,155
Publicly traded equity securities included in other current assets (4)6,3016,301—
Total$2,156,615$999,404$1,157,211

The following footnotes reference lines in our condensed consolidated balance sheets:

(1)Included in cash and cash equivalents.
(2)$16.9 million was included in cash and cash equivalents, with the difference included in short-term investments.
(3)Included in short-term investments.
(4)Included in other current assets.
(5)$33.0 million was included in cash and cash equivalents, with the difference included in short-term investments.

Index

Convertible Notes

Our 1.75% Notes,0% Notes and 0.125% Notes had a fair value of $634.4 million, $649.6 million and $43.4 million at June 30, 2024, respectively. Our 1.75% Notes,0% Notes and 0.125% Notes had a fair value of $661.1 million, $667.8 million and $42.4 million at December 31, 2023, respectively. We determine the fair value of our notes based on quoted market prices for these notes, which are Level 2 measurements because the notes do not trade regularly.

  1. Stock-based Compensation Expense

The following table summarizes stock-based compensation expense for the three and six months ended June 30, 2024 and 2023 (in thousands):

Three Months Ended June 30,Six Months Ended June 30,
2024202320242023
Cost of sales$246$118$450$237
Research, development and patent expense22,76619,24944,99138,816
Selling, general and administrative expense7,7167,19416,62714,457
Total stock-based compensation expense$30,728$26,561$62,068$53,510

As of June 30, 2024, total unrecognized estimated stock-based compensation expense related to non-vested stock options, RSUs and PRSUs was $61.6 million, $96.7 million and $13.8 million, respectively. Our actual expenses may differ from these estimates because we will adjust our unrecognized stock-based compensation expense for future forfeitures, including any PRSUs that do not vest. We expect to recognize the cost of stock-based compensation expense related to our non-vested stock options, RSUs and PRSUs over a weighted average amortization period of 1.3 years,1.6 years and 1.9 years, respectively.

Refer to Part IV, Item 15, Note 1, Organization and Significant Accounting Policies, of our audited financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2023 for further details on how we determine the fair value of stock options granted, RSUs, PRSUs and stock purchase rights under the ESPP.

For the six months ended June 30, 2024 and 2023, we used the following weighted-average assumptions in our Black-Scholes calculations:

Employee Stock Options:

Six Months Ended June 30,
20242023
Risk-free interest rate4.1%3.6%
Dividend yield0.0%0.0%
Volatility43.9%47.3%
Expected life6.3 years6.3 years

ESPP:

Six Months Ended June 30,
20242023
Risk-free interest rate5.3%5.2%
Dividend yield0.0%0.0%
Volatility38.4%36.7%
Expected life6 months6 months

RSUs:

The weighted-average grant date fair value of RSUs granted to employees for the six months ended June 30, 2024 and 2023 was $52.60 and $39.50 per share, respectively.

Index

PRSUs:

Under the terms of the PRSUs we granted in 2024 and 2023,100 percent of the PRSUs may vest at the end of thethree-year performance period based on our relative TSR as compared to a peer group of companies and as measured at the end of the performance period. Under the terms of the grants, no number of PRSUs is guaranteed to vest and the actual number of PRSUs that will vest at the end of each performance period may be anywhere from zero to 200 percent of the target number depending on our relative TSR.

The weighted-average grant date fair value of PRSUs we granted to our executive officers for the six months ended June 30, 2024 and 2023 was $78.41 and $58.99 per share, respectively.

  1. Income Taxes

We recorded income tax expense of $0.1 million and $0.1 million for the three and six months ended June 30, 2024, respectively, compared to $7.8 million and $19.2 million for the same periods in 2023, respectively. The decrease in income tax expense relates primarily to the impact of the royalty purchase agreement with Royalty Pharma on income tax expense for the three and six months ended June 30, 2023. We reflected the Royalty Pharma transaction as a taxable sale, which required us to include the proceeds from the sale, net of currently deductible issuance costs, as taxable income in 2023.

We continue to maintain a full valuation allowance on all our net deferred tax assets.

  1. Liability Related to Sale of Future Royalties

In January 2023, we entered into a royalty purchase agreement with Royalty Pharma to monetize a portion of our future SPINRAZA and pelacarsen royalties we are entitled to under our arrangements with Biogen and Novartis, respectively. As a result, we received an upfront payment of $500 million and we are eligible to receive up to $625 million in additional milestone payments. Under the terms of the agreement, Royalty Pharma will receive 25 percent of our SPINRAZA royalty payments from 2023 through 2027, increasing to 45 percent of royalty payments in 2028, on up to $1.5 billion in annual sales. In addition, Royalty Pharma will receive 25 percent of any future royalty payments on pelacarsen, our medicine in development to treat patients with elevated lipoprotein(a)-driven cardiovascular disease. Royalty Pharma’s royalty interest in SPINRAZA will revert to us after total SPINRAZA royalty payments to Royalty Pharma reach either $475 million or $550 million, depending on the timing and occurrence of FDA approval of pelacarsen.

We recorded the upfront payment of $500 million as a liability related to the sale of future royalties, net of transaction costs of $10.4 million, which we are amortizing over the estimated life of the arrangement using the effective interest rate method. We recognize royalty revenue in the period in which the counterparty sells the related product and recognizes the related revenue. We record royalty payments made to Royalty Pharma as a reduction of the liability.

We determine the effective interest rate used to record interest expense under this agreement based on an estimate of future royalty payments to Royalty Pharma. As of June 30, 2024, the estimated effective interest rate under the agreement was 13.5 percent.

The following table sets forth information on our liability related to sale of future royalties (in thousands):

Proceeds from sale of future royalties in January 2023$500,000
Issuance costs related to sale of future royalties(10,434)
Royalty payments to Royalty Pharma(44,628)
Interest expense related to sale of future royalties68,238
Amortization of issuance costs related to sale of future royalties560
Net liability related to sale of future royalties as of December 31, 2023513,736
Royalty payments to Royalty Pharma(16,236)
Interest expense related to sale of future royalties35,949
Amortization of issuance costs related to sale of future royalties305
Net liability related to sale of future royalties as of June 30, 2024$533,754

There are numerous factors, most of which are not within our control, that could materially impact the amount and timing of royalty payments from Biogen and Novartis, and result in changes to our estimate of future royalty payments to Royalty Pharma. Such factors include, but are not limited to, the commercial sales of SPINRAZA, the regulatory approval and commercial sales of pelacarsen, competing products or other significant events.

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  1. Convertible Debt

1.75 Percent Convertible Senior Notes

In 2023, we completed a $575.0 million offering of convertible senior notes and used $488.2 million of the net proceeds from the issuance of the 1.75% Notes to repurchase $504.4 million in principal of our 0.125% Notes. We expect to use the remaining net proceeds to settle the 0.125% Notes that remain outstanding and for general corporate and working capital purposes.

At June 30, 2024, we had the following 1.75% Notes outstanding (in millions except interest rate and price per share data):

1.75% Notes
Outstanding principal balance$575.0
Unamortized debt issuance costs$11.4
Maturity dateJune 2028
Interest rate1.75%
Effective interest rate2.3%
Conversion price per share$53.73
Total shares of common stock subject to conversion10.7

0 Percent Convertible Senior Notes and Call Spread

At June 30, 2024, we had the following 0% Notes outstanding (in millions except interest rate and price per share data):

0% Notes
Outstanding principal balance$632.5
Unamortized debt issuance costs$5.5
Maturity dateApril 2026
Interest rate0%
Effective interest rate0.5%
Conversion price per share$57.84
Effective conversion price per share with call spread$76.39
Total shares of common stock subject to conversion10.9

In conjunction with the 2021 offering, we entered into a call spread transaction, which was comprised of purchasing note hedges and selling warrants, to minimize the impact of potential economic dilution upon conversion of our 0% Notes by increasing the effective conversion price on our 0% Notes. We increased our effective conversion price to $76.39 with the same number of underlying shares as our 0%Notes. The call spread cost us $46.9 million, of which $136.7 million was for the note hedge purchase, offset by $89.8 million we received for selling the warrants. Similar to our 0% Notes, our note hedges are subject to adjustment. Additionally, our note hedges are exercisable upon conversion of the 0% Notes. The note hedges will expire upon maturity of the 0% Notes, or April 2026. The note hedges and warrants are separate transactions and are not part of the terms of our 0% Notes. The holders of the 0% Notes do not have any rights with respect to the note hedges and warrants.

We recorded the amount we paid for the note hedges and the amount we received for the warrants in additional paid-in capital in our condensed consolidated balance sheets. Refer to Part IV, Item 15, Note 1, Organization and Significant Accounting Policies, of our audited financial statements included in our Annual Report on Form 10-K for the year ended December 31, 2023 for our Call Spread accounting policy. We reassess our ability to continue to classify the note hedges and warrants in shareholders’ equity at each reporting period.

0.125 Percent Convertible Senior Notes and Call Spread

As discussed above, in 2023, we repurchased $504.4 million of our 0.125% Notes.

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At June 30, 2024, we had the following 0.125% Notes outstanding with interest payable semi-annually (in millions except interest rate and price per share data):

0.125% Notes
Outstanding principal balance$44.5
Unamortized debt issuance costs$0.1
Maturity dateDecember 2024
Interest rate0.125%
Effective interest rate0.5%
Conversion price per share$83.28
Effective conversion price per share with call spread$123.38
Total shares of common stock subject to conversion, excluding shares related to 0.125% Notes that we have repurchased and are currently holding in treasury0.5

In conjunction with the issuance of our 0.125% Notes in 2019, we entered into a call spread transaction, which was comprised of purchasing note hedges and selling warrants, to minimize the impact of potential economic dilution upon conversion of our 0.125% Notes by increasing the effective conversion price on our 0.125% Notes. We increased our effective conversion price to $123.38 with the same number of underlying shares as our 0.125% Notes. The call spread cost us $52.6 million, of which $108.7 million was for the note hedge purchase, offset by $56.1 million we received for selling the warrants. Similar to our 0.125% Notes, our note hedges are subject to adjustment. Additionally, our note hedges are exercisable upon conversion of the 0.125% Notes. The note hedges will expire upon maturity of the 0.125% Notes, or December 2024. The note hedges and warrants are separate transactions and are not part of the terms of our 0.125% Notes. The holders of the 0.125% Notes do not have any rights with respect to the note hedges and warrants. As of June 30, 2024, the note hedges and warrants remain outstanding.

We recorded the amount we paid for the note hedges and the amount we received for the warrants in additional paid-in capital in our condensed consolidated balance sheets. We reassess our ability to continue to classify the note hedges and warrants in shareholders’ equity at each reporting period.

Other Terms of Convertible Senior Notes

The 1.75%,0% and 0.125% Notes are convertible under certain conditions, at the option of the note holders. We can settle conversions of the notes, at our election, in cash, shares of our common stock or a combination of both. We may not redeem the notes prior to maturity, and we do not have to provide a sinking fund for them. Holders of the notes may require us to purchase some or all of their notes upon the occurrence of certain fundamental changes, as set forth in the indentures governing the notes, at a purchase price equal to 100 percent of the principal amount of the notes to be purchased, plus any accrued and unpaid interest.

  1. Legal Proceedings

From time to time, we are involved in legal proceedings arising in the ordinary course of our business. Periodically, we evaluate the status of each legal matter and assess our potential financial exposure. If we consider the potential loss from any legal proceeding to be probable and we can reasonably estimate the amount, we accrue a liability for the estimated loss. The outcome of any proceeding is not determinable in advance. Therefore, we are required to use significant judgment to determine the probability of a loss and whether the amount of the loss is reasonably estimable. Our assessment of a potential liability and the amount of accruals we recorded are based only on the information available to us at the time. As additional information becomes available, we reassess the potential liability related to the legal proceeding and may revise our estimates.

There are no pending material legal proceedings to which we are a party or of which our property is the subject.

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