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Healthcare

Spyre Therapeutics Inc.

11/18/2024 | Press release | Distributed by Public on 11/18/2024 15:10

Amendment to Quarterly Report Form 10 Q/A

syre-20240930

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

____________________________

FORM 10-Q/A

(Amendment No. 1)

____________________________

(Mark One)


x	QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 2024


o	TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from to

Commission File Number: 001-37722

____________________________

SPYRE THERAPEUTICS, INC.

(Exact Name of Registrant as Specified in its Charter)

____________________________


Delaware	46-4312787
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

221 Crescent Street Building 23, Suite 105 Waltham, MA 02453
(Address of principal executive offices including zip code)

Registrant's telephone number, including area code: (617) 651-5940

Former name, former address and former fiscal year, if changed since last report: N/A

____________________________

Securities registered pursuant to Section 12(b) of the Exchange Act:


Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common Stock, $0.0001 Par Value Per Share	SYRE	The Nasdaq Stock Market LLC (Nasdaq Global Select Market)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes xNo o

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes xNo o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company, or an emerging growth company. See the definitions of "large accelerated filer," "accelerated filer," "smaller reporting company," and "emerging growth company" in Rule 12b-2 of the Exchange Act.


Large accelerated filer	o	Accelerated filer	o
Non-accelerated filer	x	Smaller reporting company	x
		Emerging growth company	o

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes oNo x

As of November 1, 2024, the registrant had 51,431,220 shares of common stock, $0.0001 par value per share, outstanding.

EXPLANATORY NOTE

This Amendment No. 1 on Form 10-Q/A (this "Amendment") amends the Quarterly Report on Form 10-Q of Spyre Therapeutics, Inc. (the "Company") for the period ended September 30, 2024, as filed with the Securities and Exchange Commission on November 7, 2024 (the "Original Filing").

Subsequent to the filing of its Form 10-Q for the three and nine months ended September 30, 2024, the Company became aware of a misapplication of Generally Accepted Accounting Principles in the United States ("U.S. GAAP") as it relates to the Company's exclusion of its Series A non-voting convertible preferred stock and Series B non-voting convertible preferred stock in the calculation of basic and diluted net loss per share and a finding of a material weakness in internal control over financial reporting solely related to such matter. This Amendment is being filed for the sole purpose of amending certain disclosures from the Original Filing related to the aforementioned misapplication of U.S. GAAP and related finding of material weakness in internal control over financial reporting.

Specifically, this Amendment amends: (i) Part I, Item 1. "Financial Information (unaudited)" to update the Company's Consolidated Statement of Operations and related footnote disclosures for the three and nine months ended September 30, 2024, (ii) Part I, Item 4. "Controls and Procedures" to address management's re-evaluation of disclosure controls and procedures as of September 30, 2024 and to reflect the identification of a material weakness in our internal control over financial reporting and (iii) Part II, Item 6. "Exhibits" to include, in accordance with Rule 12b-15 under the Securities Exchange Act of 1934, as amended (the "Exchange Act"), updated certifications from our Chief Executive Officer and Chief Financial Officer as required by Sections 302 and 906 of the Sarbanes-Oxley Act of 2002 as Exhibits 31.1, 31.2 and 32.1. In accordance with Rule 12b-15 under the Exchange Act, this Amendment amends and restates in their entirety each item identified in the paragraph above.

Other than as described above, this Amendment does not amend, update or change any other items or disclosures contained in the Original Filing, and accordingly, all other information contained in this Amendment is as of the date of the original filing and does not reflect subsequent information or events beyond the original filing date, November 7, 2024. Accordingly, this Amendment should be read in conjunction with other filings made with the SEC subsequent to the filing of the Original Filing, including any amendments to those filings. Capitalized terms used but not defined herein shall have the meanings ascribed to such terms in the Original Filing.

SPYRE THERAPEUTICS, INC.

QUARTERLY REPORT ON FORM 10-Q

FOR THE QUARTER ENDED SEPTEMBER 30, 2024

TABLE OF CONTENTS


Page No.
PART I. FINANCIAL INFORMATION	1

Item 1.	Financial Statements (Unaudited)	1

	Condensed Consolidated Balance Sheets as of September 30, 2024 and December 31, 2023	1

	Condensed Consolidated Statements of Operations for the Three and Nine Months Ended September 30, 2024 and 2023	2

	Condensed Consolidated Statements of Comprehensive Loss for the Three and Nine Months Ended September 30, 2024 and 2023	3

	Condensed Consolidated Statements of Changes in Convertible Preferred Stock and Stockholders' Equity for the Three and Nine Months Ended September 30, 2024 and 2023	4

	Condensed Consolidated Statements of Cash Flows for the Nine Months Ended September 30, 2024 and 2023	7

	Notes to Unaudited Condensed Consolidated Financial Statements	8

Item 4.	Controls and Procedures	28

PART II. OTHER INFORMATION	30

Item 6.	Exhibits	30

Signatures	31

PART I. - Financial Information

Item 1. Financial Statements (Unaudited).

Spyre Therapeutics, Inc.

Condensed Consolidated Balance Sheets

(Unaudited, in thousands, except share and per share amounts)


September 30, 2024	December 31, 2023
ASSETS
CURRENT ASSETS
Cash and cash equivalents	$	71,580	$	188,893
Marketable securities	342,647	150,384
Prepaid expenses and other current assets	6,852	2,251
Total current assets	421,079	341,528
Restricted cash	-	322
Other non-current assets	10	9
TOTAL ASSETS	$	421,089	$	341,859

LIABILITIES AND STOCKHOLDERS' EQUITY
CURRENT LIABILITIES
Accounts payable	$	5,165	$	896
CVR liability	24,740	1,390
Accrued and other current liabilities	13,153	13,108
Related party accounts payable and other current liabilities	14,481	16,584
Total current liabilities	57,539	31,978
Non-current CVR liability	36,160	41,310
TOTAL LIABILITIES	93,699	73,288
Commitments and Contingencies (Note 7 and 8)
Series B non-voting convertible preferred stock, $0.0001 par value; 150,000 shares authorized, issued, and outstanding as of December 31, 2023.	-	84,555
STOCKHOLDERS' EQUITY
Series A non-voting convertible preferred stock, $0.0001 par value; 1,086,341 shares authorized as of September 30, 2024 and December 31, 2023; 346,045 and 437,037 shares issued and outstanding as of September 30, 2024 and December 31, 2023, respectively.	146,425	184,927
Series B non-voting convertible preferred stock, $0.0001 par value; 271,625 shares authorized and 16,667 shares issued and outstanding as of September 30, 2024.	9,395	-
Preferred stock, $0.0001 par value; 8,642,034 shares and 8,763,659 shares authorized as of September 30, 2024 and December 31, 2023, respectively; no shares issued and outstanding as of September 30, 2024 and December 31, 2023.	-	-
Common stock, $0.0001 par value; 400,000,000 shares authorized as of September 30, 2024 and December 31, 2023; 51,395,608 shares and 36,057,109 shares issued and outstanding as of September 30, 2024 and December 31, 2023, respectively.	12	10
Additional paid-in capital	1,086,237	763,191
Accumulated other comprehensive income	1,457	302
Accumulated deficit	(916,136)	(764,414)
TOTAL STOCKHOLDERS' EQUITY	327,390	184,016
TOTAL LIABILITIES, CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS' EQUITY	$	421,089	$	341,859

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

Spyre Therapeutics, Inc.

Condensed Consolidated Statements of Operations

(Unaudited, in thousands, except share and per share amounts)


	Three Months Ended September 30,	Nine Months Ended September 30,
	2024	2023	2024	2023
Revenue:
Development fee and royalty	$	-	$	-	$	-	$	886
Total revenue	-	-	-	886

Operating expenses:
Research and development (1)	44,744	24,660	112,308	55,822
General and administrative	10,648	8,584	35,005	25,874
Acquired in-process research and development	-	(298)	-	130,188
Gain on sale of in-process research and development asset	-	(14,609)	-	(14,609)
Total operating expenses	55,392	18,337	147,313	197,275
Loss from operations	(55,392)	(18,337)	(147,313)	(196,389)

Other (expense) income:
Interest income	5,184	1,251	15,536	2,021
Change in fair value of forward contract liability	-	(25,360)	-	(83,530)
Other (expense) income, net	(18,802)	2,342	(19,895)	2,262
Total other (expense) income	(13,618)	(21,767)	(4,359)	(79,247)
Loss before income tax expense	(69,010)	(40,104)	(151,672)	(275,636)
Income tax (expense) benefit	(18)	(3)	(50)	26
Net loss	$	(69,028)	$	(40,107)	$	(151,722)	$	(275,610)

Net loss per share, basic and diluted, Series A Preferred Stock (restated)	$	(42.22)	$	(34.28)	$	(95.68)	$	(586.00)
Weighted-average Series A non-voting convertible preferred stock outstanding, basic and diluted (restated)	346,045	1,062,542	383,903	371,286

Net loss per share, basic and diluted, Series B Preferred Stock (restated)	$	(42.24)	$	-	$	(95.68)	$	-
Weighted-average Series B non-voting convertible preferred stock outstanding, basic and diluted (restated)	16,667	-	95,158	-

Net loss per share, basic and diluted, common (restated)	$	(1.06)	$	(0.86)	$	(2.39)	$	(14.65)
Weighted-average common shares outstanding, basic and diluted	50,889,433	4,293,812	44,263,746	3,961,546

(1)Includes $7.7 million and $34.2 million in related party expenses for the three and nine months ended September 30, 2024, respectively, and $19.4 million and $20.8 million related party expenses for the three and nine months ended September 30, 2023, respectively.

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

Spyre Therapeutics, Inc.

Condensed Consolidated Statements of Comprehensive Loss

(Unaudited, in thousands)


Three Months Ended September 30,	Nine Months Ended September 30,
2024	2023	2024	2023
Net loss	$	(69,028)	$	(40,107)	$	(151,722)	$	(275,610)
Other comprehensive (loss) income:
Foreign currency translation adjustment	17	(29)	37	(1)
Unrealized gain (loss) on marketable securities	1,993	(114)	1,118	(83)
Total comprehensive loss	$	(67,018)	$	(40,250)	$	(150,567)	$	(275,694)

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

Spyre Therapeutics, Inc.

Condensed Consolidated Statements of Changes in

Convertible Preferred Stock and Stockholders' Equity

(Unaudited, in thousands)


Three and Nine Months Ended September 30, 2024
Series B Non-Voting Convertible Preferred Stock	Series A Non-Voting Convertible Preferred Stock	Series B Non-Voting Convertible Preferred Stock	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit	Total Stockholders' Equity
Shares	Amount	Shares	Amount	Shares	Amount	Shares	Amount
Balances - December 31, 2023	150	$	84,555	437	$	184,927	-	$	-	36,057	$	10	$	763,191	$	302	$	(764,414)	$	184,016
Issuance of Series B non-voting convertible preferred stock in connection with private placement, net of financing costs	122	168,850	-	-	-	-	-	-	-	-	-	-
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	-	-	-	-	-	-	572	-	4,390	-	-	4,390
Stock-based compensation expense	-	-	-	-	-	-	-	-	8,385	-	-	8,385
Foreign currency translation adjustment	-	-	-	-	-	-	-	-	-	16	-	16
Unrealized loss on marketable securities	-	-	-	-	-	-	-	-	-	(681)	-	(681)
Net loss	-	-	-	-	-	-	-	-	-	-	(43,857)	(43,857)
Balances - March 31, 2024	272	$	253,405	437	$	184,927	-	-	36,629	$	10	$	775,966	$	(363)	$	(808,271)	$	152,269
Stockholder approval of the issuance of Common Stock upon conversion of Series B convertible non-voting preferred stock	(272)	(253,405)	272	253,405	-	-	-	-	-	253,405
Exchange of Series A non-voting convertible preferred stock for common stock	-	-	(91)	(38,502)	-	-	3,640	1	38,501	-	-	-
Conversion of Series B non-voting convertible preferred stock into common stock	-	-	(255)	(244,010)	10,198	1	244,009	-	-	-
Issuance of common stock in connection with exercise of pre-funded warrants	-	-	-	-	-	-	250	-	1	-	-	1
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	-	-	-	-	-	-	66	-	494	-	-	494
Stock-based compensation expense	-	-	-	-	-	-	-	-	7,243	-	-	7,243
Foreign currency translation adjustment	-	-	-	-	-	-	-	-	-	4	-	4
Unrealized loss on marketable securities	-	-	-	-	-	-	-	-	-	(194)	-	(194)
Net loss	-	-	-	-	-	-	-	-	-	-	(38,837)	(38,837)
Balances - June 30, 2024	-	-	346	$	146,425	17	$	9,395	50,783	$	12	$	1,066,214	$	(553)	$	(847,108)	$	374,385


Issuance of common stock in connection with at-the-market offerings, net of offering costs	-	-	-	-	-	-	426	-	11,750	-	-	11,750
Vesting of restricted stock units	-	-	-	-	-	-	34	-	-	-	-	-
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	-	-	-	-	-	-	153	-	1,318	-	-	1,318
Stock-based compensation expense	-	-	-	-	-	-	-	-	6,955	-	-	6,955
Foreign currency translation adjustment	-	-	-	-	-	-	-	-	-	17	-	17
Unrealized gain on marketable securities	-	-	-	-	-	-	-	-	-	1,993	-	1,993
Net loss	-	-	-	-	-	-	-	-	-	-	(69,028)	(69,028)
Balances - September 30, 2024	-	-	346	$	146,425	17	$	9,395	51,396	$	12	$	1,086,237	$	1,457	$	(916,136)	$	327,390


Three and Nine Months Ended September 30, 2023
Series A Non-Voting Convertible Preferred Stock	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit	Total Stockholders' Equity
Shares	Amount	Shares	Amount
Balances - December 31, 2022	-	$	-	2,614	$	6	$	475,971	$	(48)	$	(425,624)	$	50,305
Issuance of common stock in connection with employee stock purchase plan	-	-	2	-	18	-	-	18
Stock-based compensation expense	-	-	-	-	1,709	-	-	1,709
Foreign currency translation adjustment	-	-	-	-	-	10	-	10
Unrealized gain on marketable securities	-	-	-	-	-	32	-	32
Net loss	-	-	-	-	-	-	(18,422)	(18,422)
Balances - March 31, 2023	-	$	-	2,616	$	6	$	477,698	$	(6)	$	(444,046)	$	33,652
Issuance of Series A non-voting convertible preferred stock in connection with private placement, net of financing costs	721	197,323	-	-	-	-	-	-
Issuance of common stock forward in connection with the asset acquisition of Spyre	-	-	-	-	3,768	-	-	3,768
Issuance of common stock in connection with exercise of pre-funded warrants	-	-	624	-	-	-	-	-
CVR distribution to common stockholders	-	-	-	-	(29,500)	-	-	(29,500)
Stock-based compensation expense	-	-	-	-	1,775	-	-	1,775
Foreign currency translation adjustment	-	-	-	-	-	18	-	18
Unrealized loss on marketable securities	-	-	-	-	-	(1)	-	(1)
Net loss	-	-	-	-	(217,081)	(217,081)
Balances - June 30, 2023	721	$	197,323	3,240	$	6	$	453,741	$	11	$	(661,127)	$	(207,369)
Issuance of Series A non-voting convertible preferred stock in connection with the asset acquisition of Spyre and settlement of related forward contract	365	189,741	-	-	-	-	-	-
Settlement of financing costs in connection with private placement of Series A non-voting convertible preferred stock	-	41	-	-	-	-	-	-
Issuance of common stock in connection with the asset acquisition of Spyre and settlement of related forward contract	-	-	518	1	(1)	-	-	-
Issuance of common stock in connection with exercise of pre-funded warrants	-	-	281	-	-	-	-	-
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	-	10	-	105	-	-	105
CVR distribution to common stockholders	-	-	-	-	-	-	-	-
Stock-based compensation expense	-	-	-	-	2,112	-	-	2,112
Foreign currency translation adjustment	-	-	-	-	-	(29)	-	(29)
Unrealized loss on marketable securities	-	-	-	-	-	(114)	-	(114)
Net loss	-	-	-	-	-	-	(40,107)	(40,107)
Balances - September 30, 2023	1,086	$	387,105	4,049	$	7	$	455,957	$	(132)	$	(701,234)	$	(245,402)

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

Spyre Therapeutics, Inc.

Condensed Consolidated Statements of Cash Flows

(Unaudited, in thousands)


	Nine Months Ended September 30,
	2024	2023
CASH FLOWS FROM OPERATING ACTIVITIES
Net loss	$	(151,722)	$	(275,610)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation	35,617	8,405
Acquired in-process research and development	-	130,188
Change in fair value of CVR liability	19,630	(1,300)
Change in fair value of forward contract liability	-	83,530
Gain on sale of in-process research and development asset	-	(14,609)
Lease ROU asset and leasehold improvement impairment loss	-	2,580
Loss on disposal of long-lived assets	-	915
Net accretion of discount on marketable securities	(8,985)	(612)
Interest proceeds from maturities of zero coupon US Treasury Bills	581	-
Depreciation and amortization	-	744
Amortization of operating lease assets	-	220
Other	-	18
Changes in operating assets and liabilities:
Accounts payable	4,268	1,001
Accrued and other liabilities	(257)	(4,000)
Related party accounts payable	(15,138)	(2,115)
Prepaid expenses and other assets	(4,205)	3,310
Deferred revenue	-	575
Development receivables	-	212
Operating lease liabilities	-	(2,326)
Net cash used in operating activities	(120,211)	(68,874)

CASH FLOWS FROM INVESTING ACTIVITIES
Proceeds from maturities and sales of marketable securities	183,419	21,000
Purchases of marketable securities	(366,160)	(112,631)
Cash assumed from asset acquisition of Spyre	-	3,035
Proceeds from sale of in-process research & development asset	-	15,000
Proceeds from sale of property and equipment	-	475
Net cash used in investing activities	(182,741)	(73,121)

CASH FLOWS FROM FINANCING ACTIVITIES
Proceeds from issuance of Series B non-voting convertible preferred stock in connection with private placement, net of placement and other offering costs	168,850	-
Proceeds from issuance of Series A non-voting convertible preferred stock in connection with private placement, net of placement and other offering costs	-	197,364
Proceeds from issuance of common stock in connection with at-the-market offerings, net of issuance costs	11,760	-
Payment of deferred offering costs in connection with shelf registration	(78)
Payments related to contingent value rights liability	(1,430)	-
Proceeds from employee stock option exercises, employee stock plan purchases, and exercise of prefunded warrants	6,203	123
Principal payments on finance lease obligation	-	(16)
Net cash provided by financing activities	185,305	197,471
Effect of exchange rate on cash, cash equivalents, and restricted cash	12	7
NET (DECREASE) INCREASE IN CASH, CASH EQUIVALENTS, AND RESTRICTED CASH	(117,635)	55,483

CASH, CASH EQUIVALENTS, AND RESTRICTED CASH
Beginning of period	189,215	36,416
End of period	$	71,580	$	91,899

(Continued on next page)


	Nine Months Ended September 30,
	2024	2023
Supplemental Disclosure of Non-Cash Investing and Financing Information:
Exchange of Series A non-voting convertible preferred stock for common stock	$	38,502	$	-
Conversion of Series B non-voting convertible preferred stock into common stock	$	244,010	$	-
Unpaid amounts related to issuance of common stock in connection with at-the-market offerings, net of offering costs	$	329	$	-
Allocation of deferred offering costs against proceeds of issuance of common stock	$	10	$	-

Reconciliation of Cash, Cash Equivalents, and Restricted Cash Reported in the Statement of Financial Position
Cash and cash equivalents	$	71,580	$	90,592
Restricted cash	-	1,307
Total cash, cash equivalents, and restricted cash shown in the statement of cash flows	$	71,580	$	91,899

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

Spyre Therapeutics, Inc.

Notes to Unaudited Condensed Consolidated Financial Statements

1. The Company and Basis of Presentation

Spyre Therapeutics, Inc., formerly Aeglea BioTherapeutics, Inc. ("Spyre" or the "Company"), is a clinical stage biotechnology company focused on developing next generation therapeutics for patients living with inflammatory bowel disease. The Company was formed as a Limited Liability Company ("LLC") in Delaware on December 16, 2013 under the name Aeglea BioTherapeutics Holdings, LLC and was converted from a Delaware LLC to a Delaware corporation on March 10, 2015. On November 27, 2023, the Company completed its corporate rebranding, changing the name of the Company to Spyre Therapeutics, Inc. The Company operates in one segment and has its principal offices in Waltham, Massachusetts.

On September 8, 2023, the Company effected a reverse stock split of its Common Stock at a ratio of 1-for-25 (the "Reverse Split"). Except as indicated otherwise, all share numbers related to the Company's Common Stock disclosed in these financial statements have been adjusted on a post-Reverse Split basis.

On April 12, 2023, based on the review of the inconclusive interim results from the Company's Phase 1/2 clinical trial of pegtarviliase for the treatment of Classical Homocystinuria and other business considerations, the Company announced that it had initiated a process to explore strategic alternatives to maximize stockholder value and engaged an independent exclusive financial advisor to support this process. As a result, in April 2023, the Company implemented a restructuring plan resulting in an approximate 83% reduction of the Company's existing headcount.

On June 22, 2023, the Company acquired, in accordance with the terms of the Agreement and Plan of Merger (the "Acquisition Agreement"), the assets of Spyre Therapeutics, Inc. ("Pre-Merger Spyre"), a privately held biotechnology company advancing a pipeline of antibody therapeutics with the potential to transform the treatment of inflammatory bowel disease through a research and development option agreement ("Paragon Agreement") with Paragon Therapeutics, Inc. ("Paragon"). The asset acquisition was accomplished through a two-step reverse triangular merger whereby a wholly owned subsidiary of the Company merged with and into Pre-Merger Spyre, which existed at the time the Acquisition Agreement was entered into, and became a wholly owned subsidiary of the Company in accordance with the terms of the Acquisition Agreement. Immediately following this merger, Pre-Merger Spyre merged with and into a second wholly owned subsidiary of the Company ("Merger Sub") in accordance with the terms of the Acquisition Agreement and Pre-Merger Spyre ceased to exist. Subsequently, Aeglea BioTherapeutics, Inc. was renamed Spyre Therapeutics, Inc. and is a different entity than Pre-Merger Spyre, which ceased to exist upon merging with Merger Sub. The transaction was structured as a stock-for-stock transaction pursuant to which all of Pre-Merger Spyre's outstanding equity interests were exchanged based on a fixed exchange ratio of 0.5494488 to 1 for consideration from the Company of 517,809 shares of common stock, par value of $0.0001 per share ("Common Stock"), and 364,887 shares of Series A non-voting convertible preferred stock, par value of $0.0001 per share ("Series A Preferred Stock") (convertible on a 40 to 1 basis), in addition to the assumption of outstanding and unexercised stock options to purchase 2,734 shares of Common Stock from the Amended and Restated Spyre 2023 Equity Incentive Plan (the "Asset Acquisition"). The Common Stock and Series A Preferred Stock related to the Asset Acquisition were issued to the Pre-Merger Spyre stockholders on July 7, 2023.

In connection with the Asset Acquisition, on June 26, 2023, the Company completed a private placement of shares of Series A Preferred Stock (the "June 2023 PIPE") to a group of investors (the "June 2023 Investors"). The Company sold an aggregate of 721,452 shares of Series A Preferred Stock for an aggregate purchase price of approximately $210.0 million before deducting approximately $12.7 million in placement agent and other offering expenses (together with the Asset Acquisition, the "Transactions").

In connection with the Asset Acquisition, a non-transferable contingent value right ("CVR") was distributed to stockholders of record of the Company as of the close of business on July 3, 2023 (the "Legacy Stockholders"), but was not distributed to the holders of shares of Common Stock or Series A Preferred Stock issued to the former stockholders of Pre-Merger Spyre or the June 2023 Investors in the Transactions. Holders of the CVRs will be entitled to receive cash payments from proceeds received by the Company for a three-year

period related to the disposition or monetization of its legacy assets for a period of one-year following the closing of the Asset Acquisition.

On November 21, 2023, the Company's stockholders approved the issuance of Common Stock upon conversion of the Company's Series A Preferred Stock to Common Stock. A total of 649,302 shares of Series A Preferred Stock automatically converted to 25,972,080 shares of Common Stock; 437,037 shares of Series A Preferred Stock did not automatically convert and remained outstanding after the conversion.

On December 11, 2023, the Company completed a private placement of shares of Common Stock and Series B non-voting convertible preferred stock, par value of $0.0001 per share ("Series B Preferred Stock") (convertible on a 40 to 1 basis) (the "December 2023 PIPE") to a group of investors. The Company sold an aggregate of 6,000,000 shares of Common Stock and 150,000 shares of Series B Preferred Stock for an aggregate purchase price of approximately $180.0 million before deducting approximately $10.9 million of placement agent and other offering expenses.

On March 20, 2024, the Company completed a private placement of Series B Preferred Stock (convertible on a 40 to 1 basis) (the "March 2024 PIPE") to a group of investors. The Company sold 121,625 shares of Series B Preferred Stock for a purchase price of $180.0 million before deducting approximately $11.2 million of placement agent and other offering costs.

On April 23, 2024, the Company entered into an exchange agreement with Fairmount Healthcare Fund II L.P. (the "Stockholder"), pursuant to which the Stockholder agreed to exchange an aggregate of 90,992 shares of Series A Preferred Stock for an aggregate of 3,639,680 shares of Common Stock (the "April 2024 Exchange"). The Common Stock issued in connection with the April 2024 Exchange was issued without registration under the Securities Act of 1933, as amended (the "Securities Act") in reliance on the exemption from registration contained in Section 3(a)(9) of the Securities Act. The April 2024 Exchange closed on April 25, 2024, with 346,045shares of Series A Preferred Stock remaining outstanding following the April 2024 Exchange.

On May 14, 2024, the Company's stockholders approved the issuance of Common Stock upon conversion of the Company's Series B Preferred Stock to Common Stock. A total of 254,958 shares of Series B Preferred Stock automatically converted to 10,198,320 shares of Common Stock; 16,667 shares of Series B Preferred Stock did not automatically convert and remained outstanding as of September 30, 2024.

On September 6, 2024, the Company filed a new shelf registration statement on Form S-3 that was declared effective by the SEC for the potential offering, issuance and sale by the Company of up to $500.0 million of our common stock, preferred stock, debt securities, warrants and/or units consisting of all or some of these securities. Concurrent with the filing of the shelf-registration statement, the Company entered into a sales agreement with TD Securities (USA) LLC ("TD Cowen"), as its sales agent, pursuant to which the Company may issue and sell shares of its common stock for an aggregate offering price of up to $200.0 million under an at-the-market ("ATM') offering program included in the shelf registration. In September 2024, the Company sold 426,287 shares of common stock under the ATM at a price per share of $28.15, resulting in net proceeds of $11.8 million.

Liquidity

The Company is a clinical stage biotechnology company with a limited operating history, and due to its significant research and development expenditures, the Company has generated operating losses since its inception and has not generated any revenue from the commercial sale of any products. There can be no assurance that profitable operations will ever be achieved, and, if achieved, whether profitability can be sustained on a continuing basis.

Since its inception and through September 30, 2024, the Company has funded its operations by raising an aggregate of approximately $1.1 billion of gross proceeds from the sale and issuance of convertible preferred stock and common stock, pre-funded warrants, the collection of grant proceeds, and the licensing of its product rights for commercialization of pegzilarginase in Europe and certain countries in the Middle East. As of September 30, 2024, Spyre had an accumulated deficit of $916.1 million, and cash, cash equivalents, and marketable securities of $414.2 million.

Based on current operating plans, the Company has sufficient resources to fund operations for at least one year from the issuance date of these financial statements with existing cash, cash equivalents, and marketable securities. Spyre will need to secure additional financing in the future to fund additional research and development, and before a commercial drug can be produced, marketed and sold. If the Company is unable to obtain additional financing or generate license or product revenue, the lack of liquidity could have a material adverse effect on the Company.

Basis of Presentation

The consolidated financial statements have been prepared in conformity with generally accepted accounting principles in the United States ("U.S. GAAP") as defined by the Financial Accounting Standards Board and include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.

Reclassification of Prior Year Presentation

Certain prior year amounts have been reclassified for consistency with the current year presentation. These reclassifications had no effect on the reported results of operations or balance sheets.

Unaudited Interim Financial Information

The interim condensed consolidated financial statements included in this Quarterly Report on Form 10-Q are unaudited. The unaudited interim financial statements have been prepared on the same basis as the annual financial statements and reflect, in the opinion of management, all adjustments of a normal and recurring nature that are necessary for a fair statement of the Company's financial position as of September 30, 2024, and its results of operations for the three and nine months ended September 30, 2024 and 2023, changes in convertible preferred stock and stockholders' equity for the three and nine months ended September 30, 2024 and 2023, and cash flows for the nine months ended September 30, 2024 and 2023. The results of operations for the three and nine months ended September 30, 2024, are not necessarily indicative of the results to be expected for the year ending December 31, 2024 or for any other future annual or interim period. The December 31, 2023 balance sheet was derived from audited financial statements, but does not include all disclosures required by U.S. GAAP for complete financial statements. These financial statements should be read in conjunction with the audited financial statements included in the Company's Form 10-K for the year ended December 31, 2023 (the "Annual Report") as filed with the SEC on February 29, 2024 and amended on March 1, 2024 and November 18, 2024.

2. Summary of Significant Accounting Policies

These interim condensed consolidated financial statements have been prepared in accordance with U.S. GAAP and SEC instructions for interim financial information, and should be read in conjunction with the Company's Annual Report. Significant accounting policies and other disclosures normally provided have been omitted since such items are disclosed in the Company's Annual Report. The Company uses the same accounting policies in preparing quarterly and annual financial statements.

Other than policies noted below, there have been no significant changes from the significant accounting policies and estimates disclosed in the Notes titled "1. The Company and Basis of Presentation" and "2. Summary of Significant Accounting Policies" of the Company's Annual Report.

License Agreements Contingent Milestone Payments

The Company's license agreements include specific development, regulatory, and clinical milestone payments that are payable upon the resolution of a contingency, such as upon the selection of a development candidate, first dosing of a human patient in clinical trials or receipt of the Food Drug and Administration's ("FDA") approval of a Spyre drug. The achievement of these milestone payments involves many factors outside of the Company's control and therefore the associated likelihood cannot be considered probable until the

related contingency is resolved. Based on the preceding, the Company accrues each milestone payment upon the achievement of the applicable milestone event.

Recently Adopted Accounting Pronouncements

There have been no recent accounting pronouncements or changes in accounting pronouncements during the nine months ended September 30, 2024 that are of significance or potential significance to the Company.

Not Yet Adopted Accounting Pronouncements

In November 2024, the Financial Accounting Standards Board issued ASU 2024-03 to require more detailed information about specified categories of expenses (purchases of inventory, employee compensation, depreciation, amortization, and depletion) included in certain expense captions presented on the face of the income statement. This ASU is effective for fiscal years beginning after December 15, 2026, and for interim periods within fiscal years beginning after December 15, 2027. Early adoption is permitted. The amendments may be applied either (1) prospectively to financial statements issued for reporting periods after the effective date of this ASU or (2) retrospectively to all prior periods presented in the financial statements. The Company is currently evaluating the impact this ASU will have on our disclosures.

3. Fair Value Measurements

The Company measures and reports certain financial instruments as assets and liabilities at fair value on a recurring basis. The following tables set forth the fair value of the Company's financial assets and liabilities at fair value on a recurring basis based on the three-tier fair value hierarchy (in thousands):


September 30, 2024
Level 1	Level 2	Level 3	Total
Financial Assets:
Money market funds	$	69,900	$	-	$	-	$	69,900
U.S. government treasury securities	140,072	-	-	140,072
U.S. government agency securities	-	100,328	-	100,328
Commercial paper	-	75,717	-	75,717
Corporate bonds	-	26,530	-	26,530
Total financial assets	$	209,972	$	202,575	$	-	$	412,547

Liabilities:
Parapyre Option Obligation	$	-	$	13,035	$	-	$	13,035
CVR liability	-	-	60,900	60,900
Total liabilities	$	-	$	13,035	$	60,900	$	73,935


December 31, 2023
Level 1	Level 2	Level 3	Total
Financial Assets:
Money market funds	$	150,648	$	-	$	-	$	150,648
U.S. government treasury securities	32,843	-	-	32,843
U.S. government agency securities	-	16,257	-	16,257
Commercial paper	-	104,141	-	104,141
Corporate bonds	-	33,064	-	33,064
Total financial assets	$	183,491	$	153,462	$	-	$	336,953

Liabilities:
CVR liability	$	-	$	-	$	42,700	$	42,700
Total liabilities	$	-	$	-	$	42,700	$	42,700

The Company measures the fair value of money market funds and U.S. government treasury securities on quoted prices in active markets for identical assets or liabilities. The Level 2 assets include U.S. government agency securities, commercial paper and corporate bonds, and are valued based on quoted prices for similar assets in active markets and inputs other than quoted prices that are derived from observable market data. The Company evaluates transfers between levels at the end of each reporting period. There were no transfers between Level 1, Level 2, or Level 3 during the periods presented.

Parapyre Option Obligation

Under the Paragon Agreement, the Company is obligated to issue Parapyre Holding LLC ("Parapyre") an annual equity grant of warrants, on the last business day of each of the years ended December 31, 2023 and December 31, 2024, to purchase 1% of the then outstanding shares of the Company's Common Stock, on a fully diluted basis, during the term of the Paragon Agreement (the "Parapyre Option Obligation"). The Company determined that the 2023 and 2024 grants are two separate grants, as there would be no obligation for the 2024 grant had the Company exercised or terminated all of the options under the Paragon Agreement prior to December 31, 2023. The service inception period for the grant precedes the grant date, with the full award being vested as of the grant date with no post-grant date service requirement. Accordingly, a liability related to the Parapyre Option Obligation is recorded pursuant to the Paragon Agreement during interim periods. On December 31, 2023, the Company settled its 2023 obligation under the Parapyre Option Obligation by issuing Parapyre 684,407 warrants to purchase the Company's Common Stock, with a $21.52 per share exercise price for each warrant.

The Parapyre Option Obligation is considered a Level 2 liability based on observable market data for substantially the full term of the liability. The Parapyre Option Obligation is measured each period using a Black-Scholes model to estimate the fair value of the option grant. Changes in the fair value of the Parapyre Option Obligation are recorded as stock-based compensation within Research and development expenses for non-employees who provided pre-clinical development services.

CVR Liability

In connection with the Asset Acquisition, a non-transferable CVR was distributed to the Legacy Stockholders, but was not distributed to holders of shares of Common Stock or Series A Preferred Stock issued to the June 2023 Investors or former stockholders of Pre-Merger Spyre in connection with the Transactions. Holders of the CVR will be entitled to receive certain cash payments from proceeds received by the Company for a three-year period, if any, related to the disposition or monetization of the Company's legacy assets for a period of one year following the closing of the Asset Acquisition.

The fair value of the CVR liability was determined using the probability weighted discounted cash flow method to estimate future cash flows associated with the sale of the legacy assets. Analogous to a dividend being declared/approved in one period and paid out in another, the liability was recorded at the date of approval, June 22, 2023, as a Common Stock dividend, returning capital to the Legacy Stockholders. Changes in fair

value of the liability will be recognized as a component of Other income (expense) in the consolidated statement of operations and comprehensive loss in each reporting period. The liability value is based on significant inputs not observable in the market such as estimated cash flows, estimated probabilities of regulatory success, and discount rates, which represent a Level 3 measurement within the fair value hierarchy.

The significant inputs used to estimate the fair value of the CVR liability were as follows:


	September 30, 2024
Estimated cash flow dates	05/28/25 - 06/22/26
Estimated probability of success	72% - 100%
Estimated reimbursement rate compared to reimbursement target	81% - 100%
Risk-adjusted discount rates	7.76% - 7.82%

The change in fair value between December 31, 2023 and September 30, 2024 was a $19.6 million increase, primarily driven by changes in the likelihood of achievement of certain milestones and the time value of money, partially offset by an increase in risk-adjusted discount rates.

The following table presents changes in the CVR liability for the periods presented (in thousands):


	CVR Liability
Beginning balance as of December 31, 2023	$	42,700
Changes in the fair value of the CVR liability	19,630
Payments	(1,430)
Ending Balance as of September 30, 2024	$	60,900

Forward Contract Liability

In connection with the Asset Acquisition, the Company entered into a contract for the issuance of 364,887 shares of Series A Preferred Stock as part of the consideration transferred. This forward contract was classified as a liability because the underlying preferred shares were contingently redeemable. The forward contract was carried at fair value on the balance sheet, with changes in fair value between the acquisition date and June 30, 2023 recorded in earnings. The liability was settled with the issuance of the Series A Preferred Stock on July 7, 2023.

The fair value of the forward contract as of the acquisition date, June 22, 2023, was $106.2 million. The liability was settled with the issuance of the Series A Preferred Stock on July 7, 2023 for $189.7 million. For the three and nine months ended September 30, 2023, $25.4 million and $83.5 million, respectively, was recorded as Other (expense) income in the consolidated statements of operations in connection with the change in fair value of the forward contract liability.

4. Cash Equivalents and Marketable Securities

The following tables summarize the estimated fair value of the Company's cash equivalents and marketable securities and the gross unrealized gains and losses (in thousands):


September 30, 2024
Amortized Cost	Gross Unrealized Gains	Gross Unrealized Losses	Estimated Fair Value
Cash equivalents:
Money market funds	$	69,900	$	-	$	-	$	69,900
Total cash equivalents	$	69,900	$	-	$	-	$	69,900

Marketable securities:
Commercial paper	$	75,503	$	214	$	-	$	75,717
Corporate bonds	26,457	76	(3)	26,530
U.S. government treasury securities	139,313	768	(9)	140,072
U.S. government agency securities	99,973	363	(8)	100,328
Total marketable securities	$	341,246	$	1,421	$	(20)	$	342,647


December 31, 2023
Amortized Cost	Gross Unrealized Gains	Gross Unrealized Losses	Estimated Fair Value
Cash equivalents:
Money market funds	$	150,648	$	-	$	-	$	150,648
Commercial paper	24,950	5	-	24,955
U.S. government treasury securities	10,965	1	-	10,966
Total cash equivalents	$	186,563	$	6	$	-	$	186,569

Marketable securities:
Commercial paper	$	79,124	$	62	$	-	$	79,186
Corporate bonds	32,984	81	(1)	33,064
U.S. government treasury securities	21,846	31	-	21,877
U.S. government agency securities	16,147	110	-	16,257
Total marketable securities	$	150,101	$	284	$	(1)	$	150,384

The following table summarizes the available-for-sale securities in an unrealized loss position for which an allowance for credit losses has not been recorded as of September 30, 2024 and December 31, 2023, aggregated by major security type and length of time in a continuous unrealized loss position:


September 30, 2024
Less Than 12 Months	12 Months or Longer	Total
Fair Value	Unrealized Losses	Fair Value	Unrealized Losses	Fair Value	Unrealized Losses
Corporate bonds	$	1,952	$	(3)	$	-	$	-	$	1,952	$	(3)
U.S. government treasury securities	17,517	(9)	-	-	17,517	(9)
U.S. government agency securities	18,101	(8)	-	-	18,101	(8)
Total marketable securities	$	37,570	$	(20)	$	-	$	-	$	37,570	$	(20)

December 31, 2023
Less Than 12 Months	12 Months or Longer	Total
Fair Value	Unrealized Losses	Fair Value	Unrealized Losses	Fair Value	Unrealized Losses
Corporate bonds	$	9,907	$	(1)	$	-	$	-	$	9,907	$	(1)
U.S. government treasury securities	4,831	-	-	-	4,831	-
Total marketable securities	$	14,738	$	(1)	$	-	$	-	$	14,738	$	(1)

The Company evaluated its securities for credit losses and considered the decline in market value to be primarily attributable to current economic and market conditions and not to a credit loss or other factors. Additionally, the Company does not intend to sell the securities in an unrealized loss position and does not expect it will be required to sell the securities before recovery of the unamortized cost basis. As of September 30, 2024 and December 31, 2023, an allowance for credit losses had not been recognized. Given the Company's intent and ability to hold such securities until recovery, and the lack of significant change in credit risk of these investments, the Company does not consider these marketable securities to be impaired as of September 30, 2024 and December 31, 2023.

The financial instruments that potentially subject the Company to a concentration of credit risk consist principally of cash deposits. Accounts at each of our two U.S. banking institutions are insured by the Federal Deposit Insurance Corporation ("FDIC") up to $250,000 per depositor. As of September 30, 2024 and December 31, 2023, cash deposits at the Company's U.S. banking institutions exceeded the FDIC limits. Uninsured foreign cash deposits were immaterial for both periods.

There were no realized gains or losses on marketable securities for the three and nine months ended September 30, 2024 and 2023. Interest on marketable securities is included in interest income. Accrued interest receivable on available-for-sale debt securities as of September 30, 2024 and December 31, 2023, was $1.7 million and $0.9 million, respectively, and is reflected in Prepaid expenses and other current assets.

The following table summarizes the contractual maturities of the Company's marketable securities at estimated fair value (in thousands):


September 30, 2024	December 31, 2023
Due in one year or less	$	253,613	$	115,784
Due in 1 - 2 years	89,034	34,600
Total marketable securities	$	342,647	$	150,384

The Company may sell investments at any time for use in current operations even if they have not yet reached maturity. As a result, the Company classifies marketable securities, including securities with maturities beyond twelve months as current assets.

5. Accrued and Other Current Liabilities

Accrued and other current liabilities consist of the following (in thousands):


September 30, 2024	December 31, 2023
Accrued compensation	$	3,966	$	4,054
Accrued contracted research and development costs	7,527	7,092
Accrued professional and consulting fees	1,134	1,474
Accrued other	526	488
Total accrued and other current liabilities	$	13,153	$	13,108

6. Asset Acquisition

On June 22, 2023, the Company acquired Pre-Merger Spyre pursuant to the Acquisition Agreement, by and among the Company, Aspen Merger Sub I, Inc., a Delaware corporation and a wholly owned subsidiary of the Company ("First Merger Sub"), Sequoia Merger Sub II, LLC, a Delaware limited liability company and wholly owned subsidiary of the Company ("Second Merger Sub"), and Pre-Merger Spyre. Pursuant to the Acquisition Agreement, First Merger Sub merged with and into Pre-Merger Spyre, pursuant to which Pre-Merger Spyre was the surviving corporation and became a wholly owned subsidiary of the Company (the "First Merger"). Immediately following the First Merger, Pre-Merger Spyre merged with and into Second Merger Sub, pursuant to which Second Merger Sub became the surviving entity. Pre-Merger Spyre was a pre-clinical stage biotechnology company that was incorporated on April 28, 2023 under the direction of Peter Harwin, a Managing Member of Fairmount, for the purpose of holding rights to certain intellectual property being developed by Paragon. Fairmount is a founder of Paragon.

The Company completed the Asset Acquisition of Pre-Merger Spyre, in accordance with the terms of the Acquisition Agreement. Under the terms of the Acquisition Agreement, the Company issued 517,809 shares of Common Stock and 364,887 shares of Series A Preferred Stock to former Pre-Merger Spyre security holders. In addition, outstanding and unexercised stock options to purchase 2,734 shares of common stock were assumed from the Amended and Restated Spyre 2023 Equity Incentive Plan.

At the acquisition date, the Company recorded forward contracts to represent the obligation to issue shares of Common Stock and shares of Series A Preferred Stock, respectively. The forward contract related to the Common Stock was recorded as Additional paid-in capital as the instrument is indexed to the Common Stock. The forward contract related to the Series A Preferred Stock was recorded as a liability, as the underlying stock has a cash redemption feature. On July 7, 2023, both the shares of Common Stock and Series A Preferred Stock were issued and the forward contract liability associated with the Series A Preferred Stock was settled accordingly.

The Company concluded that the arrangement met the definition of an asset acquisition rather than a business combination, as substantially all of the fair value of the gross assets acquired was concentrated in a single identifiable asset, Pre-Merger Spyre's option to exclusively license certain intellectual property rights (the "Option"). The Company determined that the Option was a single asset as the Company's strategy relied on developing the entire portfolio of individual treatments to create combination treatments that simultaneously address different mechanisms of inflammatory bowel disease with a single treatment. The Company also determined that the pipeline candidates within the portfolio were similar in nature and risk profile. In addition, the Company did not obtain any substantive processes, assembled workforce, or employees capable of producing outputs in connection with the Asset Acquisition.

The Company determined that the cost to acquire the asset was $113.2 million which was recorded as acquired in-process research and development ("IPR&D"). The fair value of the consideration issued consisted of the 364,887 shares of Series A Preferred Stock (14,595,480 shares of Common Stock on an as-converted basis) and 517,809 shares of Common Stock, valued at $291.08 per share and $7.277 per share, respectively.

The Asset Acquisition costs are shown on the following table (in millions):


June 22, 2023
Consideration transferred in Series A Preferred Stock and Common Stock	$	110.0
Transaction costs incurred by Pre-Merger Spyre	3.2
Total cost to acquire asset	$	113.2

The allocation of the purchase price to net assets acquired is as a follows:


June 22, 2023
Acquired in-process research and development	$	130.2
Cash acquired	3.0
Assumed liabilities	(20.0)
Total cost to acquire asset	$	113.2

7. Licensing Agreements

On July 12, 2023, December 14, 2023, and June 5, 2024, the Company exercised the Option available under the Paragon Agreement with respect to the SPY001, SPY002, and SPY003 research programs, respectively.

On May 14, 2024, the Company and Paragon entered into (i) a license agreement (the "SPY001 License Agreement"), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting α4ß7 integrin and (ii) a license agreement (the "SPY002 License Agreement"), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting TL1A, respectively.

On October 11, 2024, the Company and Paragon entered into a license agreement (the "SPY003 License Agreement" and, together with the SPY001 License Agreement and the SPY002 License Agreement, the "License Agreements"), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting IL-23 in the field of IBD.

Under the terms of each License Agreement, the Company is obligated to pay Paragon up to $22.0 million based on specific development, regulatory and clinical milestones for the first product under each agreement, respectively, that achieves such specified milestones, including a $1.5 million fee for nomination of a development candidate, as applicable, and a further milestone payment of $2.5 million upon the first dosing of a human patient in a Phase 1 trial. In addition, the following summarizes other key terms of each License Agreement:

•Paragon will provide the Company with an exclusive license (such license, with respect to the SPY003 License Agreement only, being limited to the field of IBD) to its patents covering the related antibody, the method of use and its method of manufacture.

•Paragon will not conduct any new campaigns that generate anti-α4ß7 or anti-TL1A monospecific antibodies in any field or anti-IL-23 monospecific antibodies in the field of IBD, in each case for at least 5 years.

•The Company will pay Paragon a low single-digit percentage royalty for single antibody products and a mid single-digit percentage royalty for products containing more than one antibody from Paragon.

•There is a royalty step-down of 1/3rd if there is no Paragon patent in effect during the royalty term.

•The royalty term ends on the later of (i) the last-to-expire licensed patent or Company patent directed to the manufacture, use or sale of a licensed antibody in the country at issue or (ii) 12 years from the date of first sale of a Company product.

•Agreement may be terminated on 60 days' notice by the Company; on material breach without cure; and to the extent permitted by law, on a party's insolvency or bankruptcy.

•With respect to the SPY002 License Agreement only, on a product by product basis, the Company will pay sublicensing fees of up to approximately $20 million upon the achievement of mostly commercial milestones.

The Company recognizes the expense associated with each milestone when the achievement of the milestone is deemed probable. During the three and nine months ended September 30, 2024, the Company recognized expense of nil and $5.5 million related to Paragon license milestone payments recorded within Research and development expenses in the accompanying condensed statement of operations. There was no such expense for the three and nine months ended September 30, 2023.

For the three and nine months ended September 30, 2024, the Company made cash milestone payments to Paragon totaling $2.5 million and $5.5 million, respectively. As of September 30, 2024, there were no Paragon license milestone payments outstanding and payable to Paragon.

Additionally, the Company recognized $0.3 million and $0.4 million related to sublicensing fees and which was recorded as Research and development expenses in the accompanying condensed statement of operations for the three and nine months ended September 30, 2024, respectively. As of September 30, 2024, $0.3 million in sublicensing fees were outstanding and payable to Paragon.

8. Related Party Transactions

Paragon and Parapyre each beneficially own less than 5% of the Company's capital stock through their respective holdings of the Company's Common Stock. Fairmount Funds Management LLC ("Fairmount") beneficially owns more than 5% of the Company's capital stock on an as-converted basis, has two seats on the Company's board of directors (the "Board") and beneficially owns more than 5% of Paragon, which is a joint venture between Fairmount and FairJourney Biologics. Fairmount appointed Paragon's board of directors and has the contractual right to approve the appointment of any executive officers. Parapyre is an entity formed by Paragon as a vehicle to hold equity in Spyre in order to share profits with certain employees of Paragon.

The following is the summary of expenses related to the Paragon Agreement and License Agreements, which are ultimately settled in cash (in millions) and recorded within Research and development in the consolidated statement of operations for the periods presented:


Three Months Ended September 30,	Nine Months Ended September 30,
2024	2023	2024	2023
Reimbursable costs under the Paragon Agreement	$	1.3	$	16.7	$	15.3	$	17.9
License Agreements milestone and sublicensing fees	0.3	-	5.9	-
Total related party expense (excludes stock comp)	$	1.6	$	16.7	$	21.2	$	17.9

The following is the summary of Related party accounts payable and other current liabilities (in millions):


September 30, 2024	December 31, 2023
Reimbursable costs under the Paragon Agreement	$	1.2	$	16.6
Parapyre warrants liability	13.0	-
License Agreements development milestone liability (see Note 7)	0.3	-
Total related party accounts payable	$	14.5	$	16.6

Paragon Agreement

In connection with the Asset Acquisition, the Company assumed the rights and obligations of Pre-Merger Spyre under the Paragon Agreement. Under the Paragon Agreement, Spyre is obligated to compensate Paragon for its services performed under each research program based on the actual costs incurred with mark-up costs pursuant to the terms of the Paragon Agreement. Spyre is also obligated under the Paragon Agreement to issue Parapyre annual equity grants of warrants in accordance with the Parapyre Option Obligation.

On July 12, 2023, December 14, 2023, and June 5, 2024, the Company exercised the Option available under the Paragon Agreement with respect to the SPY001, SPY002 and SPY003 research programs, respectively. Our Option available under the Paragon Agreement with respect to the SPY004 program remains unexercised. Please refer to Note 7 for additional information on the License Agreements related to the exercised options.

On May 14, 2024, the Company, Paragon and Parapyre entered into a second amended and restated antibody discovery and option agreement that amends and restates that certain amended and restated antibody discovery and option agreement, dated September 29, 2023, by and between Paragon, Parapyre and Spyre Therapeutics, LLC, in order to, among other things, (i) replace the Company's subsidiary with the Company as a party to the agreement and (ii) amend certain terms related to the SPY003 research program, including without limitation, (a) establishing an SPY003 antibody selection process pursuant to which the Company and Paragon shall alternate in turn to select a project antibody to be included and excluded, respectively, from the Company's rights under its option to license certain intellectual property rights related to SPY003 from Paragon until all project antibodies under the SPY003 research program have been selected; (b) reducing the development costs invoiced to the Company for the SPY003 research program incurred from and after April 1, 2024 through completion of the SPY003 antibody selection process by 50%; (c) requiring Paragon to reimburse the Company for 50% of the development costs for the SPY003 research program incurred prior to April 1, 2024; provided, that Paragon receives rights to at least one SPY003 project antibody following completion of the SPY003 antibody selection process; (d) obligating the Company to exercise its option to license the intellectual property rights to SPY003 project antibodies and technology following the completion of the SPY003 antibody selection process; and (e) establishing a license agreement term sheet for the SPY003 research program with substantially similar milestone payment terms and royalty payment terms as the SPY001 License Agreement. Please refer to Note 7 for additional disclosures.

For the three and nine months ended September 30, 2024, the Company recognized expenses related to services provided by Paragon totaling $7.4 million and $28.3 million, respectively, which included $6.1 million and $13.0 million, respectively, of stock-based compensation expense, and were recorded as Research and development expenses in the consolidated statements of operations. Included within the expenses recognized for services provided by Paragon for the nine months ended September 30, 2024, is a $5.9 million reduction in Research and development expenses related to the reimbursement of 50% of the development costs for the SPY003 research program by Paragon.

For the three and nine months ended September 30, 2024, the Company made payments totaling $1.2 million and $30.7 million respectively, in connection with the Paragon Agreement.

Parapyre Option Obligation

Pursuant to the Paragon Agreement, the Company agreed to issue Parapyre an annual equity grant of warrants, on the last business day of each of the years ended December 31, 2023 and December 31, 2024, to purchase 1% of the then outstanding shares of the Company's Common Stock, on a fully diluted basis, during the term of the Paragon Agreement. See Note 10 for disclosures related to the Parapyre Option Obligation.

Paragon License Agreements

See Note 7 for disclosures related to the License Agreements entered into with Paragon.

Mark McKenna Option Grant

On February 1, 2024, the Board appointed Mark McKenna as a Class I director. Mr. McKenna and the Company are parties to a consulting agreement, pursuant to which Mr. McKenna agreed to continue to provide consulting services as an independent contractor to the Company, with an effective date of August 1, 2023 (the "Vesting Commencement Date"). As compensation for Mr. McKenna's consulting services, on November 22, 2023, he was granted non-qualified stock options to purchase 477,000 shares of the Company's Common Stock under the 2016 Plan (as defined in Note 8) with an exercise price of $10.39 per share, which vest as to 25% on the one year anniversary of the Vesting Commencement Date and thereafter vest and become exercisable in 36 equal monthly installments, subject to Mr. McKenna's continued service to the Company through each applicable vesting date. For the three and nine months ended September 30, 2024, the Company recognized $0.3 million and $0.8 million, respectively, in stock-based compensation expense related to Mr. McKenna's consulting agreement. There was no such expense for the three and nine months ended September 30, 2023.

9. Convertible Preferred Stock and Stockholders' Equity

Pre-Funded Warrants

In February 2019, April 2020 and May 2022, the Company issued pre-funded warrants to purchase the Company's Common Stock in underwritten public offerings at the offering price of the Common Stock, less the $0.0025 per share exercise price of each warrant. The warrants were recorded as a component of stockholders' (deficit) equity within additional paid-in capital and have no expiration date. Per the terms of the warrant agreements, the outstanding warrants to purchase shares of Common Stock may not be exercised if the holder's ownership of the Company's Common Stock would exceed 4.99% ("Maximum Ownership Percentage"), or 9.99% for certain holders. By written notice to the Company, each holder may increase or decrease the Maximum Ownership Percentage to any other percentage (not in excess of 19.99% for the majority of such warrants). The revised Maximum Ownership Percentage would be effective 61 days after the notice is received by the Company.

As of September 30, 2024, all pre-funded warrants have been exercised and none remain outstanding.

Parapyre Warrants

The Company settled its 2023 obligations under the Parapyre Option Obligation by issuing Parapyre 684,407 warrants to purchase the Company's Common Stock, with a $21.52 per share exercise price for each warrant. Pursuant to the terms of the warrant agreement, the outstanding warrants to purchase shares of Common Stock may not be exercised if the holder's ownership of the Company's Common Stock would exceed 4.99%. As of September 30, 2024, none of the warrants issued under the Parapyre Option Obligation have been exercised.

Series A Non-Voting Convertible Preferred Stock

On June 22, 2023, the Company filed a Certificate of Designation of Preferences, Rights and Limitations of the Series A Preferred Stock with the Secretary of State of the State of Delaware (the "Series A Certificate of Designation") in connection with the Asset Acquisition and the June 2023 PIPE.

Pursuant to the Series A Certificate of Designation, holders of Series A Preferred Stock are entitled to receive dividends on shares of Series A Preferred Stock equal to, on an as-if-converted-to-Common Stock basis, and in the same form as, dividends actually paid on shares of Common Stock. Except as provided in the Series A Certificate of Designation or as otherwise required by law, the Series A Preferred Stock does not have voting rights. However, as long as any shares of Series A Preferred Stock are outstanding, the Company will not, without the affirmative vote of the holders of a majority of the then outstanding shares of the Series A Preferred Stock: (a) alter or change adversely the powers, preferences or rights given to the Series A Preferred Stock, or alter or amend the Series A Certificate of Designation, amend or repeal any provision of, or add any provision to, the Company's Certificate of Incorporation or its Bylaws, or file any articles of amendment, certificate of designations, preferences, limitations and relative rights of any series of preferred stock, if such action would adversely alter or change the preferences, rights, privileges or powers of, or restrictions provided for the benefit of the Series A Preferred Stock, regardless of whether any of the foregoing actions will be by means of amendment to the Certificate of Incorporation or by merger, consolidation, recapitalization, reclassification, conversion or otherwise, (b) issue further shares of Series A Preferred Stock or increase or decrease (other than by conversion) the number of authorized shares of Series A Preferred Stock, (c) prior to the stockholder approval of the conversion of the Series A Preferred Stock into shares of Common Stock in accordance with Nasdaq Stock Market Rules (the "Series A Conversion Proposal") or at any time while at least 30% of the originally issued Series A Preferred Stock remains issued and outstanding, consummate (x) any Fundamental Transaction (as defined in the Series A Certificate of Designation) or (y) any merger or consolidation of the Company with or into another entity or any stock sale to, or other business combination in which our stockholders immediately before such transaction do not hold at least a majority of our capital stock immediately after such transaction or (d) enter into any agreement with respect to any of the foregoing. The Series A Preferred Stock does not have a preference upon any liquidation, dissolution or winding-up of the Company.

On June 26, 2023, the Company completed a private placement of 721,452 shares of Series A Preferred Stock in exchange for gross proceeds of approximately $210.0 million, or net proceeds of $197.3 million, after deducting placement agent and other offering costs.

On July 7, 2023, the Company issued 364,887 shares of Series A Preferred Stock as part of its consideration transferred in connection with the Asset Acquisition that closed on June 22, 2023 which settled the related forward contract liability.

On November 21, 2023, the Company's stockholders approved the Series A Conversion Proposal, among other matters, at a special meeting of stockholders. As a result of the approval of the Series A Conversion Proposal, all conditions that could have required cash redemption of the Series A Preferred Stock were satisfied. Since the Series A Preferred Stock is no longer redeemable, the associated balances of the Series A Preferred Stock were reclassified from mezzanine equity to permanent equity during the fourth quarter of 2023.

Following stockholder approval of the Series A Conversion Proposal, each share of Series A Preferred Stock automatically converted into 40 shares of Common Stock, subject to certain limitations, including that a holder of Series A Preferred Stock is prohibited from converting shares of Series A Preferred Stock into shares of Common Stock if, as a result of such conversion, such holder, together with its affiliates, would beneficially own more than a specified percentage (established by the holder between 0.0% and 19.9%) of the total number of shares of Common Stock issued and outstanding immediately after giving effect to such conversion. 649,302 shares of Series A Preferred Stock automatically converted to 25,972,080 shares of Common Stock; 437,037 shares of Series A Preferred Stock did not automatically convert and remained outstanding following the conversion. This conversion was recorded as a reclassification between Series A Preferred Stock and Common Stock based on the historical per-share contributed capital amount of the Series A Preferred Stock.

On April 23, 2024, in connection with the April 2024 Exchange, the Stockholder agreed to exchange an aggregate of 90,992 shares of Series A Preferred Stock for an aggregate of 3,639,680 shares of the Company's Common Stock. This exchange was recorded as a reclassification between Series A Preferred Stock and Common Stock based on the historical per-share contributed capital amount, inclusive of any forward-contract valuation adjustments, of the Series A Preferred Stock. Following the April 2024 Exchange, 346,045 shares of Series A Preferred Stock remained outstanding.

Series B Non-Voting Convertible Preferred Stock

On December 8, 2023, the Company filed a Certificate of Designation of Preferences, Rights and Limitations of Series B Non-Voting Convertible Preferred Stock with the Secretary of State of the State of Delaware (the "Series B Certificate of Designation") in connection with the December 2023 PIPE.

Pursuant to the Series B Certificate of Designation, holders of Series B Preferred Stock are entitled to receive dividends on shares of Series B Preferred Stock equal to, on an as-if-converted-to-Common Stock basis, and in the same form as, dividends actually paid on shares of Common Stock. Except as provided in the Series B Certificate of Designation or as otherwise required by law, the Series B Preferred Stock does not have voting rights. However, as long as any shares of Series B Preferred Stock are outstanding, the Company will not, without the affirmative vote of the holders of a majority of the then outstanding shares of the Series B Preferred Stock, alter or change adversely the powers, preferences or rights given to the Series B Preferred Stock, or alter or amend the Series B Certificate of Designation, amend or repeal any provision of, or add any provision to, the Company's Certificate of Incorporation or its Bylaws, or file any articles of amendment, certificate of designations, preferences, limitations and relative rights of any series of preferred stock, if such action would adversely alter or change the preferences, rights, privileges or powers of, or restrictions provided for the benefit of the Series B Preferred Stock, regardless of whether any of the foregoing actions will be by means of amendment to the Certificate of Incorporation or by merger, consolidation, recapitalization, reclassification, conversion or otherwise. The Series B Preferred Stock does not have a preference upon any liquidation, dissolution or winding-up of the Company.

On December 11, 2023, as part of the December 2023 PIPE, the Company completed a private placement of 150,000 shares of Series B Preferred Stock in exchange for gross proceeds of $90.0 million.

On March 18, 2024, in connection with the March 2024 PIPE, the Company filed a certificate of amendment to its Series B Certificate of Designation to increase the number of authorized shares of Series B Preferred Stock from 150,000 to 271,625.

On March 20, 2024, as part of the March 2024 PIPE, the Company completed a private placement of 121,625 shares of Series B Preferred Stock in exchange for gross proceeds of approximately $180.0 million.

On May 14, 2024, the Company's stockholders approved the issuance of Common Stock upon the conversion of all issued and outstanding Series B Preferred Stock into shares of Common Stock in accordance with the Nasdaq Stock Market Rules (the "Series B Conversion Proposal"), among other matters, at its 2024 annual meeting of stockholders. As a result of the approval of the Series B Conversion Proposal, all conditions that could have required cash redemption of the Series B Preferred Stock were satisfied. Since the Series B Preferred Stock is no longer redeemable, the associated balances of the Series B Preferred Stock were reclassified from mezzanine equity to permanent equity during the second quarter of 2024.

Following stockholder approval of the Series B Conversion Proposal, each share of Series B Preferred Stock automatically converted into 40 shares of the Common Stock, subject to certain limitations, including that a holder of Series B Preferred Stock is prohibited from converting shares of Series B Preferred Stock into shares of Common Stock if, as a result of such conversion, such holder, together with its affiliates, would beneficially own more than a specified percentage (established by the holder between 0.0% and 19.9%) of the total number of shares of Common Stock issued and outstanding immediately after giving effect to such conversion. 254,958 shares of Series B Preferred Stock automatically converted to 10,198,320 shares of Common Stock; 16,667 shares of Series B Preferred Stock did not automatically convert and remain outstanding as of September 30, 2024 due to beneficial ownership limitations. This conversion was recorded as a reclassification between Series B Preferred Stock and Common Stock based on the historical per-share contributed capital amount of the Series B Preferred Stock.

S-3 Shelf & ATM

a sales agreement (the "Sales Agreement") with TD Securities (USA) LLC ("TD Cowen"), as its sales agent, pursuant to which the Company may issue and sell shares of its common stock for an aggregate offering price of up to $200.0 million under an at-the-market ("ATM') offering program included in the shelf registration. In September 2024, the Company sold 426,287 shares of common stock under the ATM at a price per share of $28.15 resulting in net proceeds of $11.8 million. As of November 1, 2024, $188.0 million remained available for sale under the Sales Agreement.

10. Stock-Based Compensation

2015 Equity Incentive Plan

In March 2015, the Company adopted the 2015 Equity Incentive Plan ("2015 Plan"), administered by the board of directors, and provides for the Company to sell or issue share of Common Stock or restricted Common Stock, or to grant incentive stock options or nonqualified stock options for the purchase of Common Stock, to employees, members of the board of directors and consultants of the Company. The Company granted options under the 2015 Plan until April 2016 when it was terminated as to future awards, although it continues to govern the terms of options that remain outstanding under the 2015 Plan.

As of September 30, 2024, a total of 952 shares of Common Stock are subject to options outstanding under the 2015 Plan and will become available under the 2016 Equity Incentive Plan ("2016 Plan") to the extent the options are forfeited or lapse unexercised.

2016 Equity Incentive Plan

The 2016 Plan became effective in April 2016 and serves as the successor to the 2015 Plan. Under the 2016 Plan, the Company may grant stock options, stock appreciation rights, restricted stock awards, restricted stock units, performance awards, and stock bonuses. The 2016 Plan, as amended, provides for an automatic increase in the number of shares reserved for issuance thereunder on January 1 of each year for the remaining term of the plan equal to (a) 5.0% of the number of issued and outstanding shares of Common Stock (including such shares issuable pursuant to the exercise or conversion, as applicable, of any outstanding pre-funded warrants and nonvoting convertible preferred stock) on December 31 of the immediately preceding year, or (b) a lesser amount as approved by the board each year (the "Evergreen Provision"). As a result of the Evergreen Provision, on January 1, 2024 and 2023, an additional 3,023,650 and 104,561 shares, respectively, became available for issuance under the 2016 Plan.

As of September 30, 2024, the 2016 Plan had 7,228,113 shares available for future issuance, of which 3,247,677 shares were subject to outstanding option awards.

2018 Equity Inducement Plan

The 2018 Equity Inducement Plan ("2018 Plan") became effective in February 2018.

During the third quarter of 2024, the Company amended the 2018 Plan to increase the number of shares of Common Stock reserved for issuance by 1,000,000. After this amendment and as of September 30, 2024, the 2018 Plan had 6,999,445 shares available for future issuance, of which 5,624,067 shares were subject to outstanding option awards and restricted unit awards.

Service-based awards granted under the 2018 Plan, 2016 Plan, and 2015 Plan generally vest over four years and expire after ten years, although awards have been granted with vesting terms less than four years. Under the 2016 Plan and 2018 Plan, the Company may grant stock-based awards with service conditions ("service-based" awards), performance conditions ("performance-based" awards), and market conditions ("market-based" awards).

Spyre 2023 Equity Incentive Plan

On June 22, 2023, in connection with the Asset Acquisition, the Company assumed the Amended and Restated Spyre 2023 Equity Incentive Plan and its outstanding and unexercised stock options, which were

converted to options to purchase 2,734 shares of Common Stock. The acquisition-date fair value of these grants will be recognized as an expense on a pro-rata basis over the vesting period.

The following table summarizes the Company's stock awards granted under all equity incentive and inducement plans for each of the periods indicated:


Three Months Ended September 30,	Nine Months Ended September 30,
2024	2023	2024	2023
Grants	Weighted Average Grant Date Fair Value	Grants	Weighted Average Grant Date Fair Value	Grants	Weighted Average Grant Date Fair Value	Grants	Weighted Average Grant Date Fair Value
Stock options	425,500	$	25.74	1,044,667	$	14.50	1,857,853	$	28.40	3,867,366	$	9.65

Parapyre Option Obligation

As of September 30, 2024, the pro-rated estimated fair value of the options to be granted on December 31, 2024 related to the Parapyre Option Obligation, was approximately $13.0 million. For the three and nine months ended September 30, 2024, $6.1 million and $13.0 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. For the three and nine months ended September 30, 2023, $2.7 million and $2.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. As of September 30, 2024, the unamortized expense related to the Parapyre Option Obligation was $4.4 million.

2016 Employee Stock Purchase Plan

Under the Company's 2016 Employee Stock Purchase Plan ("2016 ESPP"), the Company issued and sold 14,053 and 16,383 shares during the three and nine months ended September 30, 2024, respectively, and sold 704 and 2,496 shares during the three and nine months ended September 30, 2023, respectively. The aggregate cash proceeds were not material for all periods.

Stock-based Compensation Expense

Total stock-based compensation expense recognized from the Company's equity incentive plans, 2018 Plan, 2016 ESPP and Parapyre Option Obligation during the periods presented was as follows (in thousands):


Three Months Ended September 30,	Nine Months Ended September 30,
2024	2023	2024	2023
Research and development (1)	$	8,555	$	2,965	$	18,863	$	4,136
General and administrative	4,545	1,820	16,754	4,269
Total stock-based compensation expense (2)	$	13,100	$	4,785	$	35,617	$	8,405

(1) For the three and nine months ended September 30, 2024, $6.1 million and $13.0 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. For the three and nine months ended September 30, 2023, $2.7 million and $2.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. (2) Of the total $13.1 million and $35.6 million of stock-based compensation expense for the three and nine months ended September 30, 2024, $0.1 million and $3.6 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the respective period. Of the total $4.8 million and $8.4 million of stock-based compensation expense for the three and nine months ended September 30, 2023, $0.8 million and $4.2 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the period.

The following table summarizes the weighted-average Black-Scholes option pricing model assumptions used to estimate the fair value of stock options granted under the Company's equity incentive plans, and the shares purchasable under the 2016 ESPP during the periods presented:


Three Months Ended September 30,	Nine Months Ended September 30,
2024	2023	2024	2023
Stock Options Granted
Expected term (in years)	6.08	6.08	6.02	6.04
Expected volatility	105%	101%	105%	111%
Risk-free interest	4.13%	4.28%	4.03%	4.07%
Dividend yield	-	-	-	-

2016 ESPP
Expected term (in years)	0.50	0.50	0.50	0.49
Expected volatility	71%	222%	83%	181%
Risk-free interest	5.02%	5.29%	5.15%	4.99%
Dividend yield	-	-	-	-

11. Legacy Strategic License Agreements

On March 21, 2021, the Company entered into an exclusive license and supply agreement with Immedica (the "Immedica Agreement"). On July 27, 2023, the Company announced that it had entered into an agreement to sell the global rights to pegzilarginase, an investigational treatment for the rare metabolic disease Arginase 1 Deficiency, to Immedica for $15.0 million in upfront cash proceeds and up to $100.0 million in contingent milestone payments. The sale of pegzilarginase to Immedica superseded and terminated the Immedica Agreement.

The milestone payments are contingent on formal reimbursement decisions by national authorities in key European markets and pegzilarginase approval by the FDA, among other events. In addition to the payment previously made to holders of the Company's CVRs (as defined in Note 1) related to the upfront cash proceeds, any contingent milestone payments under the Immedica Agreement, if paid within the CVR period, will be distributed to holders of the Company's CVRs net of expenses and adjustments pursuant to the contingent value rights agreement we entered into with Equiniti Trust Company LLC (f/k/a American Stock Transfer & Trust Company LLC) as rights agent in connection with the Asset Acquisition.

The Company did not recognize any revenue under the Immedica Agreement for the three and nine months ended September 30, 2024. For the nine months ended September 30, 2023, the Company recognized $0.9 million of development fee revenue in connection with the Immedica Agreement, which was attributable to the PEACE Phase 3 trial and BLA package for pegzilarginase. There was no such revenue for the three months ended September 30, 2023.

For more details on the Immedica Agreement, which was terminated on July 27, 2023, please refer to the Note under Item 1 of Part I, titled "12. Strategic License Agreements" of the Company's Annual Report.

Contract Balances from Customer Contract

The timing of revenue recognition, billings and cash collections results in contract assets and contract liabilities on the Company's balance sheets. The Company recognizes license and development receivables based on billed services, which are derecognized upon reimbursement. When consideration is received, or such consideration is unconditionally due, from a customer prior to transferring goods or services to the customer under the terms of a contract, a contract liability is recorded. Contract liabilities are recognized as revenue after control of the goods or services is transferred to the customer and all revenue recognition criteria have been met.

The Company did not have any contract assets or liabilities as of September 30, 2024 and December 31, 2023.

12. Sale of Pegzilarginase to Immedica

On July 27, 2023, the Company announced that it had entered into an agreement to sell the global rights to pegzilarginase, an investigational treatment for the rare metabolic disease Arginase 1 Deficiency, to Immedica for $15.0 million in upfront cash proceeds and up to $100.0 million in contingent milestone payments. The sale of pegzilarginase to Immedica superseded and terminated the previous license agreement between the Company and Immedica. On July 27, 2023, the carrying value of the asset was zero as it was internally developed. Accordingly the Company recognized a $14.6 million gain within operating expenses, which is the full $15.0 million in upfront cash proceeds, net of transaction costs and the derecognition of pegzilarginase related nonfinancial assets and liabilities.

The milestone payments are contingent on formal reimbursement decisions by national authorities in key European markets and pegzilarginase approval by the FDA, among other events. The upfront payment and contingent milestone payments if paid, net of expenses and adjustments, will be distributed to holders of Aeglea's CVR pursuant to the CVR Agreement resulting from the Asset Acquisition.

13. Net Loss Per Share (as restated)

Restatement

Subsequent to the filing of its Quarterly Report on Form 10-Q for the period ended September 30, 2024, management identified an error related to the calculation and presentation of loss per share. The Company had previously concluded that the Series A Preferred Stock and Series B Preferred Stock had preferences over the Company's Common Stock and were therefore excluded from the calculation of basic and dilutive net loss per share pursuant to the two-class method. The Company has now determined that the Series A Preferred Stock and Series B Preferred Stock do not have preferential rights over the Company's Common Stock and, accordingly, are considered to be a second and third class of common stock for purposes of calculating net loss per share. Consequently, the Company has now separately calculated and presented net loss per share for its Common Stock, Series A Preferred Stock and Series B Preferred Stock.

For the three months ended September 30, 2024 and 2023, loss per share attributable to common stockholders as previously presented was $1.36 and $9.34, respectively, and as restated was $1.06 and $0.86, respectively. For the nine months ended September 30, 2024 and 2023, loss per share attributable to common stockholders as previously presented was $3.43 and $69.57, respectively, and as restated was $2.39 and $14.65, respectively. Net loss per share attributable to holders of Series A Preferred Stock and Series B Preferred Stock was not previously presented. All related amounts have been updated to reflect the effects of the restatement throughout the financial statements and related footnotes, as applicable.

The Company computes net loss per share of Common Stock, Series A Preferred Stock, and Series B Preferred Stock using the two-class method required for multiple classes of common stock and other participating securities.

The two-class method is an earnings (loss) allocation method under which earnings (loss) per share is calculated for each class of common stock. The Company has determined that the Series A Preferred Stock and Series B Preferred Stock do not have preferential rights when compared to the Company's Common Stock and therefore it must allocate losses to these other classes of common stock, as illustrated in the table below.

Basic and diluted net loss per share is computed by dividing the net loss by the weighted-average number of shares and pre-funded warrants outstanding during the period, without consideration of potential dilutive securities. The pre-funded warrants are included in the computation of basic net loss per share as the exercise price is negligible and they are fully vested and exercisable. For periods in which the Company generated a net loss, the Company does not include potential shares of common stock in diluted net loss per share when the impact of these items is anti-dilutive. The Company has generated a net loss for all periods presented, therefore diluted net loss per share is the same as basic net loss per share since the inclusion of potential shares of common stock would be anti-dilutive.

The following table sets forth the computation of basic and diluted net loss per share of Common Stock, Series A Preferred Stock, and Series B Preferred Stock (in thousands, except share and per share amounts):


Three Months Ended September 30,
2024	2023
Series A Preferred Stock	Series B Preferred Stock	Common Stock	Series A Preferred Stock	Series B Preferred Stock	Common Stock
Net loss per share, basic and diluted:
Numerator
Allocation of losses	$	(14,610)	$	(704)	$	(53,714)	$	(36,427)	$	-	$	(3,680)
Denominator
Weighted-average shares outstanding	346,045	16,667	50,889,433	1,062,542	-	4,015,661
Weighted-average pre-funded warrants outstanding	-	-	-	-	-	278,151
Number of shares used in per share computation	346,045	16,667	50,889,433	1,062,542	-	4,293,812
Net loss per share, basic and diluted	$	(42.22)	$	(42.24)	$	(1.06)	$	(34.28)	$	-	$	(0.86)

Nine Months Ended September 30,
2024	2023
Series A Preferred Stock	Series B Preferred Stock	Common Stock	Series A Preferred Stock	Series B Preferred Stock	Common Stock
Net loss per share, basic and diluted:
Numerator
Allocation of losses	$	(36,733)	$	(9,105)	$	(105,884)	$	(217,573)	$	-	$	(58,037)
Denominator
Weighted-average shares outstanding	383,903	95,158	44,146,958	371,286	-	3,116,434
Weighted-average pre-funded warrants outstanding	-	-	116,788	-	-	845,112
Number of shares used in per share computation	383,903	95,158	44,263,746	371,286	-	3,961,546
Net loss per share, basic and diluted	$	(95.68)	$	(95.68)	$	(2.39)	$	(586.00)	$	-	$	(14.65)

The following weighted-average equity instruments were excluded from the calculation of diluted net loss per share because their effect would have been anti-dilutive for the periods presented:


Three Months Ended September 30,	Nine Months Ended September 30,
2024	2023	2024	2023
Options to purchase common stock	4,733,609	3,135,672	4,583,260	1,426,224
Unvested restricted stock units	65,925	-	69,503	252
Outstanding Parapyre warrants	684,407	-	684,407	-

14. Restructuring Charges

Severance and Stock Compensation

On April 12, 2023, based on the review of the inconclusive interim results from the Company's Phase 1/2 clinical trial of pegtarviliase for the treatment of classical homocystinuria and other business considerations, the Company announced that it had initiated a process to explore strategic alternatives to maximize stockholder value and engaged an independent exclusive financial advisor to support this process.

As a result, the Company implemented a restructuring plan resulting in an approximate 83% reduction of the Company's existing headcount by June 30, 2023. The Company recognized restructuring expenses consisting of cash severance payments and other employee-related costs of nil and $6.4 million during the three

and nine months ended September 30, 2023, respectively. In addition, the Company recognized $1.0 million in non-cash stock-based compensation expense related to the accelerated vesting of stock-based awards for certain employees. The Company recorded these restructuring charges based on each employee's role to the respective research and development and general and administrative operating expense categories on its condensed consolidated statements of operations and comprehensive loss.

Sale of Assets

During the second quarter of 2023, the Company sold various lab equipment, consumables, and furniture and fixtures for total consideration of $0.5 million. After recording the disposal of all property and equipment net of proceeds, the Company recorded a $0.7 million and $0.2 million loss on disposal of long lived assets within Research and development and General and administrative expenses, respectively.

Lease Right-of-use Asset and Leasehold Improvement Impairment

Effective June 30, 2023, the Company abandoned its leased office space in Austin, Texas. As a result, the Company recognized an impairment loss of $0.9 million related to the operating lease right-of-use asset and $1.7 million related to leasehold improvements. On August 7, 2023, the Company terminated its building lease in Austin, Texas. The negotiated termination agreement obligated the Company to pay the lessor a $2.0 million termination fee in exchange for releasing the Company of all further obligations under the lease.

All charges related to the restructuring activities were recognized during the second quarter of 2023. No further restructuring charges were incurred under the restructuring plan. A summary of the charges related to the restructuring activities is as follows (in thousands):


Severance Related Expenses	Stock Compensation Expenses	Loss on Disposal of Long Lived Assets	Lease Asset Impairment	Total Restructuring Costs
Research and development	$	3,182	$	123	$	749	$	1,405	$	5,459
General and administrative	3,266	870	182	1,175	5,493
Total	$	6,448	$	993	$	931	$	2,580	$	10,952

As of December 31, 2023, $1.1 million of restructuring costs remained outstanding and unpaid. As of September 30, 2024, there were no remaining liabilities under the restructuring plan described above.

15. Subsequent Events

On October 1, 2024, the Company appointed Sheldon Sloan, M.D., M. Bioethics, to serve as its Chief Medical Officer.

On October 11, 2024, the Company and Paragon entered into the SPY003 License Agreement, pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting IL-23 in the field of IBD.

Item 4. Controls and Procedures.

Disclosure Controls and Procedures

Our management, with the participation of our principal executive officer and principal financial officer, evaluated, as of the end of the period covered by this Quarterly Report on Form 10-Q, the effectiveness of our disclosure controls and procedures. The term "disclosure controls and procedures," as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act, means controls and other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC's rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports we file or submit

under the Exchange Act is accumulated and communicated to our management, including our principal executive officer and principal financial officer, as appropriate to allow timely decisions regarding required disclosure. Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and our management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

At the time the Company filed the Original Filing, our principal executive officer and principal financial officer concluded that the Company's disclosure controls and procedures were effective at the resaonable assurance level as of September 30, 2024. Subsequent to the Original Filing and solely in connection with this Amendment, our principal executive officer and principal financial officer reevaluated the effectiveness of the Company's disclosure controls and procedures and identified a material weakness in the Company's internal control over financial reporting as the Company did not design and maintain effective controls related to the earnings per share calculation. A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of a company's annual or interim financial statements will not be prevented or detected on a timely basis.

Specifically, subsequent to the Original Filing, our principal executive officer and principal financial officer concluded that our disclosure controls and procedures were not effective as of September 30, 2024 as the Company did not design and maintain effective controls related to the earnings per share calculation, as there was not an effectively designed control in place to evaluate the treatment of the Series A Preferred Stock and the Series B Preferred Stock for the purpose of calculating earnings per share under the two-class method. The material weakness resulted in the restatement of the Company's previously filed consolidated financial statements as of and for the year ended December 31, 2023, as well as the quarterly condensed consolidated financial information for the 2024 interim periods ended March 31, 2024, June 30, 2024, and September 30, 2024 related to earnings per share. Additionally, the material weakness could result in further misstatements of the earnings per share calculation that would result in a material misstatement to the annual or interim financial statements that would not be prevented or detected.

Notwithstanding the material weakness in internal control over financial reporting, our management, including our principal executive officer and the principal financial officer, have concluded that our consolidated financial statements present fairly, in all material respects, our financial position, results of our operations and our cash flows for the periods presented in this Quarterly Report, in conformity with U.S. GAAP.

Remediation Plan

Our remediation process includes, but is not limited to, enhancing the design of the control relevant to the calculation of net earnings (loss) per share calculations and disclosures to ensure that economic substance beyond the legal form of our capital structure is considered when calculating net earnings (loss) per share. We believe that these actions will remediate the material weakness. The material weakness will not be considered remediated, however, until the applicable controls operate, and management has concluded, through testing, that these controls are operating effectively.

Changes in Internal Control Over Financial Reporting

There were no changes in our internal control over financial reporting during the quarter ended September 30, 2024, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

PART II. - Other Information

Item 6. Exhibits.

The exhibits filed or furnished as part of this Quarterly Report on Form 10-Q are set forth below.


Exhibit Number	Description	Form	File No	Date of Filing	Exhibit No.	Filed Herewith
2.1	Agreement and Plan of Merger, dated June 22, 2023, by and among Aeglea BioTherapeutics, Inc. Aspen Merger Sub I, Inc., Sequoia Merger Sub II, LLC and Spyre Therapeutics, Inc.	S-1	333-276251	12/22/2023	2.1

3.1	Second Amended and Restated Certificate of Incorporation of the Company, effective as of May 14, 2024	8-K	001-37722	05/15/2024	3.2

3.2	Amended and Restated Bylaws	S-1/A	333-276251	02/05/2024	3.2

3.3	Certificate of Designation of Series A Non-Voting Convertible Preferred Stock	S-1	333-276251	12/22/2023	3.3

3.4	Certificate of Designation of Series B Non-Voting Convertible Preferred Stock	S-1	333-276251	12/22/2023	3.4

3.5	Certificate of Amendment to Certificate of Designation of Series B Non-Voting Convertible Preferred Stock	8-K	001-37722	03/18/2024	3.2

10.1#	IL-23 (SPY003) License Agreement, dated October 11, 2024, by and between the Company and Paragon Therapeutics, Inc.	8-K	001-37722	10/15/2024	10.1

10.2#	Amended and Restated Biologics Master Services Agreement, dated October 14, 2024, by and between the Company and WuXi Biologics (Hong Kong) Limited.	8-K	001-37722	10/15/2024	10.2

10.3#	Amended and Restated Cell Line License Agreement, dated October 14, 2024, by and between the Company and WuXi Biologics (Hong Kong) Limited.	8-K	001-37722	10/15/2024	10.3

10.4+*	Fifth Amendment to the Spyre Therapeutics, Inc. 2018 Equity Inducement Plan

10.5+*	Offer Letter, dated September 20, 2024, by and between the Company and Sheldon Sloan

10.6	Sales Agreement, dated September 6, 2024, between Spyre Therapeutics, Inc. and TD Securities (USA) LLC	S-3	333-281975	9/6/2024	1.2

31.1	Certification of the Principal Executive Officer pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities Exchange Act of 1934					X

31.2	Certification of the Principal Financial Officer pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities Exchange Act of 1934	X

32.1(1)	Certification of the Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002	X

101.INS	Inline XBRL Instance Document - the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document.	X

101.SCH	Inline XBRL Taxonomy Extension Schema Document	X

101.CAL	Inline XBRL Taxonomy Extension Calculation Linkbase Document	X

101.DEF	Inline XBRL Taxonomy Extension Definition Linkbase Document	X

101.LAB	Inline XBRL Taxonomy Extension Label Linkbase Document	X

101.PRE	Inline XBRL Taxonomy Extension Presentation Linkbase Document	X

104	The cover page from this Quarterly Report formatted in Inline XBRL and contained in Exhibit 101

+ Indicates management contract or compensatory plan.

* Previously filed with the Original Filing.

# Portions of this exhibit have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K.

(1)The certifications on Exhibit 32 hereto are deemed furnished and not "filed" for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that Section. Such certifications will not be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.

Signatures

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

Date: November 18, 2024


Spyre Therapeutics, Inc.

By:	/s/ Scott Burrows
Scott Burrows
Chief Financial Officer
(Principal Financial Officer and Principal Accounting Officer)

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