0001714899-22-000078 | 10-Q | XBRL Viewer

Prepaid expenses and other current assets

^[1]

$ 42,141,000

$ 7,922,000

$ 30,601,000

30,914,000

$ 30,914,000

Collaborative Arrangement | Takeda Pharmaceutical Company Limited

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Possible preclinical milestone payments (up to)

55,000,000

12,000,000

12,000,000

Preclinical milestone payment earned not yet received

Remaining performance obligation

Collaborative Arrangement | Takeda Pharmaceutical Company Limited | Maximum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Aggregate payments due upon achievement of certain clinical milestone events

280,000,000

Aggregate payments upon achievement of certain regulatory milestone events

200,000,000

Milestone payments per biologic product upon achievement of a certain sales-based milestone

75,000,000

Aggregate sales-based milestone payments, if one biologic product from each program achieves milestone

$ 150,000,000

Collaborative Arrangement | Takeda Pharmaceutical Company Limited | Milestone Triggered And Option Fee Payments

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative Arrangement | Takeda Pharmaceutical Company Limited | Milestone Triggered

53,000,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative Arrangement | Takeda Pharmaceutical Company Limited | Product

$ 12,000,000

43,000,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative Arrangement, PTV:PGRN and ATV:TREM2 | Takeda Pharmaceutical Company Limited

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Number of new contracts | contract

Collaborative Arrangement, PTV:PGRN | Takeda Pharmaceutical Company Limited

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Prepaid expenses and other current assets

2,900,000

Offset to research and development expense, cost reimbursement

2,900,000

Collaborative Arrangement, PTV:PGRN | Takeda Pharmaceutical Company Limited | Milestone Triggered

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative Arrangement, ATV:TREM2 | Takeda Pharmaceutical Company Limited

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Prepaid expenses and other current assets

2,100,000

$ 2,100,000

Offset to research and development expense, cost reimbursement

2,100,000

Collaborative Arrangement, ATV:TREM2 | Takeda Pharmaceutical Company Limited | Milestone Triggered

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative Arrangement, ATV:Tau | Takeda Pharmaceutical Company Limited

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

$ 27,900,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

$ 27,900,000

[1]	Includes related party collaboration revenue from a customer of $2.2 million and $0.9 million for the three months ended March 31, 2022 and 2021, respectively.

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Mar. 31, 2022	Dec. 31, 2021
Statement of Financial Position [Abstract]
Convertible preferred stock, par value (usd per share)	$ 0.01	$ 0.01
Convertible preferred stock, shares authorized (in shares)	40,000,000	40,000,000
Convertible preferred stock, shares issued (in shares)	0	0
Convertible preferred stock, shares outstanding (in shares)	0	0
Common stock, par value (usd per share)	$ 0.01	$ 0.01
Common stock, shares authorized (in shares)	400,000,000	400,000,000
Common stock, shares issued (in shares)	122,857,908	122,283,305
Common stock, shares outstanding (in shares)	122,857,908	122,283,305

Condensed Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit
Beginning balance (in shares) at Dec. 31, 2020		120,531,333
Beginning balance at Dec. 31, 2020	$ 1,150,531	$ 1,531	$ 1,503,660	$ (245)	$ (354,415)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuances under equity incentive plans (in shares)		334,634
Issuances under equity incentive plans	3,822	$ 3	3,819
Vesting of restricted stock units (in shares)		281,465
Vesting of restricted stock units	0	$ 3	(3)
Stock-based compensation	21,028		21,028
Net loss	(70,041)				(70,041)
Other comprehensive income (loss)	13			13
Ending balance (in shares) at Mar. 31, 2021		121,147,432
Ending balance at Mar. 31, 2021	$ 1,105,353	$ 1,537	1,528,504	(232)	(424,456)
Beginning balance (in shares) at Dec. 31, 2021	122,283,305	122,283,305
Beginning balance at Dec. 31, 2021	$ 962,291	$ 1,548	1,608,238	(2,499)	(644,996)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuances under equity incentive plans (in shares)		151,419
Issuances under equity incentive plans	1,463	$ 2	1,461
Vesting of restricted stock units (in shares)		423,184
Vesting of restricted stock units	0	$ 4	(4)
Stock-based compensation	26,145		26,145
Net loss	(65,220)				(65,220)
Other comprehensive income (loss)	$ (6,752)			(6,752)
Ending balance (in shares) at Mar. 31, 2022	122,857,908	122,857,908
Ending balance at Mar. 31, 2022	$ 917,927	$ 1,554	$ 1,635,840	$ (9,251)	$ (710,216)

Significant Accounting Policies - Narrative (Details) $ in Millions	3 Months Ended
	Mar. 31, 2022 USD ($) Segment
Accounting Policies [Abstract]
Number of operating segments \| Segment	1
Restricted cash \| $	$ 1.5

Marketable Securities - Summary of Available for Sale Securities (Details) $ in Thousands	Mar. 31, 2022 USD ($) security	Dec. 31, 2021 USD ($) security
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 1,111,736	$ 999,527
Unrealized Holding Gains	0	1
Unrealized Holding Losses	(8,899)	(2,149)
Aggregate Fair Value	1,102,837	997,379
Short-term marketable securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	856,585	572,250
Unrealized Holding Gains	0	1
Unrealized Holding Losses	(4,016)	(321)
Aggregate Fair Value	852,569	571,930
Short-term marketable securities \| U.S. government treasuries
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	703,031	450,689
Unrealized Holding Gains	0	0
Unrealized Holding Losses	(3,735)	(253)
Aggregate Fair Value	$ 699,296	$ 450,436
Number of securities held in unrealized holding loss position \| security	43	19
Aggregate fair value, unrealized holding loss position	$ 699,300	$ 450,400
Short-term marketable securities \| Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	72,422	70,076
Unrealized Holding Gains	0	1
Unrealized Holding Losses	(281)	(68)
Aggregate Fair Value	$ 72,141	$ 70,009
Number of securities held in unrealized holding loss position \| security	19	16
Aggregate fair value, unrealized holding loss position	$ 68,600	$ 68,500
Short-term marketable securities \| Commercial paper
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	81,132	51,485
Unrealized Holding Gains	0	0
Unrealized Holding Losses	0	0
Aggregate Fair Value	81,132	51,485
Long-term marketable securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	255,151	427,277
Unrealized Holding Gains	0	0
Unrealized Holding Losses	(4,883)	(1,828)
Aggregate Fair Value	250,268	425,449
Long-term marketable securities \| U.S. government treasuries
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	227,708	411,904
Unrealized Holding Gains	0	0
Unrealized Holding Losses	(4,653)	(1,757)
Aggregate Fair Value	$ 223,055	$ 410,147
Number of securities held in unrealized holding loss position \| security	18	16
Aggregate fair value, unrealized holding loss position	$ 223,100	$ 410,100
Long-term marketable securities \| Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	27,443	15,373
Unrealized Holding Gains	0	0
Unrealized Holding Losses	(230)	(71)
Aggregate Fair Value	$ 27,213	$ 15,302
Number of securities held in unrealized holding loss position \| security	5	6
Aggregate fair value, unrealized holding loss position	$ 27,200	$ 15,300

License Agreements	3 Months Ended
License Agreements	Mar. 31, 2022
Organization, Consolidation and Presentation of Financial Statements [Abstract]
License Agreements	License Agreements Genentech In June 2016, the Company entered into an Exclusive License Agreement with Genentech, Inc. (“Genentech License Agreement”). The details of the Genentech License Agreement are further described in Note 7, License Agreements, to the consolidated financial statements in the Company's 2021 Annual Report on Form 10-K. No expenses were recorded associated with the Genentech License Agreement in the three months ended March 31, 2022 or 2021.

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2022	Dec. 31, 2021
Current assets:
Cash and cash equivalents	$ 104,953	$ 293,477
Short-term marketable securities	852,569	571,930
Cost sharing reimbursements due from related party	0	1,226
Prepaid expenses and other current assets	30,914	30,601
Total current assets	988,436	897,234
Long-term marketable securities	250,268	425,449
Property and equipment, net	37,679	38,865
Operating lease right-of-use asset	30,263	30,743
Other non-current assets	14,212	11,871
Total assets	1,320,858	1,404,162
Current liabilities:
Accounts payable	3,358	4,779
Cost sharing payments due to related party	2,713	0
Accrued compensation	5,844	19,013
Accrued clinical and other research & development costs	19,283	15,887
Accrued manufacturing costs	11,366	9,955
Other accrued costs and current liabilities	2,390	2,857
Operating lease liability, current	5,659	5,453
Related party contract liability, current	290,627	292,386
Contract liabilities, current	0	27,915
Total current liabilities	341,240	378,245
Related party contract liability, less current portion	828	1,295
Contract liabilities, less current portion	3,398	3,398
Operating lease liability, less current portion	57,086	58,554
Other non-current liabilities	379	379
Total liabilities	402,931	441,871
Commitments and contingencies (Note 7)
Stockholders' equity:
Convertible preferred stock, $0.01 par value; 40,000,000 shares authorized as of March 31, 2022 and December 31, 2021; 0 shares issued and outstanding as of March 31, 2022 and December 31, 2021	0	0
Common stock, $0.01 par value; 400,000,000 shares authorized as of March 31, 2022 and December 31, 2021; 122,857,908 shares and 122,283,305 shares issued and outstanding as of March 31, 2022 and December 31, 2021, respectively	1,554	1,548
Additional paid-in capital	1,635,840	1,608,238
Accumulated other comprehensive loss	(9,251)	(2,499)
Accumulated deficit	(710,216)	(644,996)
Total stockholders' equity	917,927	962,291
Total liabilities and stockholders’ equity	$ 1,320,858	$ 1,404,162

Collaboration Agreements - Sanofi (Details) - USD ($)

1 Months Ended

3 Months Ended

42 Months Ended

Apr. 30, 2022

Mar. 31, 2022

Mar. 31, 2021

Mar. 31, 2022

Dec. 31, 2021

Sanofi | Collaborative Arrangement

^[1]

$ 42,141,000

$ 7,922,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Sanofi | Collaborative Arrangement | Alzheimer's Disease Services

$ 0

Receivable

$ 0

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Sanofi | Collaborative Arrangement | Milestone Triggered

$ 3,400,000

3,400,000

$ 3,400,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Sanofi | Collaborative Arrangement | Milestone Triggered | Subsequent Event

25,000,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Sanofi | Collaborative Arrangement | Product

$ 40,000,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Derivative Instruments and Hedging Activities Disclosure [Abstract]

$ 0

[1]	Includes related party collaboration revenue from a customer of $2.2 million and $0.9 million for the three months ended March 31, 2022 and 2021, respectively.

Derivative Financial Instruments (Tables)

3 Months Ended

Mar. 31, 2022

Summary of Forward Foreign Currency Exchange Contracts Outstanding

The following table summarizes the Company’s forward foreign currency exchange contracts outstanding as of March 31, 2022 and December 31, 2021, respectively (notional amounts in thousands):


Foreign Exchange Contracts	Number of Contracts	Aggregate Notional(1) Amount in Foreign Currency	Maturity
Euros	3	150	Apr 2022 - Jun 2022
British Pounds	3	300	Apr 2022 - Jun 2022
Total at March 31, 2022	6
Euros	7	800	Jan 2022 - Jun 2022
British Pounds	6	900	Jan 2022 - Jun 2022
Total at December 31, 2021	13

_________________________________________________

(1) The notional amount represents the net amount of foreign currency that will be received upon maturity of the forward contracts.

- Definition

Tabular disclosure of pertinent information about a derivative or group of derivatives on a disaggregated basis, such as for individual instruments, or small groups of similar instruments. May include a combination of the type of instrument, risks being hedged, notional amount, hedge designation, related hedged item, inception date, maturity date, or other relevant item.

+ References

Reference 1: http://fasb.org/us-gaap/role/ref/legacyRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4B
-URI http://asc.fasb.org/extlink&oid=125515794&loc=SL5624163-113959

Reference 2: http://fasb.org/us-gaap/role/ref/legacyRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 1B
-URI http://asc.fasb.org/extlink&oid=125515794&loc=SL5580258-113959

Reference 3: http://fasb.org/us-gaap/role/ref/legacyRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=125515794&loc=d3e41620-113959

Reference 4: http://fasb.org/us-gaap/role/ref/legacyRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 1A
-URI http://asc.fasb.org/extlink&oid=125515794&loc=SL5579245-113959

Reference 5: http://fasb.org/us-gaap/role/ref/legacyRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=125515794&loc=d3e41638-113959

Reference 6: http://fasb.org/us-gaap/role/ref/legacyRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 8
-URI http://asc.fasb.org/extlink&oid=125515794&loc=d3e41678-113959

Reference 7: http://fasb.org/us-gaap/role/ref/legacyRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=125515794&loc=d3e41641-113959

Reference 8: http://fasb.org/us-gaap/role/ref/legacyRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4C
-URI http://asc.fasb.org/extlink&oid=125515794&loc=SL5624171-113959

Reference 9: http://fasb.org/us-gaap/role/ref/legacyRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=125515794&loc=SL5579240-113959

+ Details

Marketable Securities

3 Months Ended

Mar. 31, 2022

Investments, Debt and Equity Securities [Abstract]

Marketable Securities

All marketable securities were considered available-for-sale at March 31, 2022 and December 31, 2021. On a recurring basis, the Company records its marketable securities at fair value using Level 1 or Level 2 inputs as discussed in Note 2, "Fair Value Measurements". The amortized cost, gross unrealized holding gains or losses, and fair value of the Company’s marketable securities by major security type at each balance sheet date are summarized in the tables below (in thousands):


	March 31, 2022
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries(1)	$	703,031	$	—	$	(3,735)	$	699,296

Corporate debt securities(2)	72,422		—		(281)		72,141
Commercial paper	81,132		—		—		81,132
Total short-term marketable securities	856,585		—		(4,016)		852,569
Long-term marketable securities:
U.S. government treasuries(3)	227,708		—		(4,653)		223,055

Corporate debt securities(4)	27,443		—		(230)		27,213
Total long-term marketable securities	255,151		—		(4,883)		250,268
Total	$	1,111,736	$	—	$	(8,899)	$	1,102,837

__________________________________________________

(1)Unrealized holding losses on 43 securities with an aggregate fair value of $699.3 million.

(2)Unrealized holding losses on 19 securities with an aggregate fair value of $68.6 million.

(3)Unrealized holding losses on 18 securities with an aggregate fair value of $223.1 million.

(4)Unrealized holding losses on 5 securities with an aggregate fair value of $27.2 million.


	December 31, 2021
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries(1)	$	450,689	$	—	$	(253)	$	450,436

Corporate debt securities(2)	70,076		1		(68)		70,009
Commercial paper	51,485		—		—		51,485
Total short-term marketable securities	572,250		1		(321)		571,930
Long-term marketable securities:
U.S. government treasuries(3)	411,904		—		(1,757)		410,147

Corporate debt securities(4)	15,373		—		(71)		15,302
Total long-term marketable securities	427,277		—		(1,828)		425,449
Total	$	999,527	$	1	$	(2,149)	$	997,379

__________________________________________________

(1)Unrealized holding losses on 19 securities with an aggregate fair value of $450.4 million.

(2)Unrealized holding losses on 16 securities with an aggregate fair value of $68.5 million.

(3)Unrealized holding losses on 16 securities with an aggregate fair value of $410.1 million.

(4)Unrealized holding losses on 6 security with an aggregate fair value of $15.3 million.

As of March 31, 2022 and December 31, 2021, some of the Company's marketable securities were in an unrealized loss position. The Company has not recognized an allowance for credit losses as of March 31, 2022 or December 31, 2021. The Company determined that it had the ability and intent to hold all marketable securities that have been in a continuous loss position until maturity or recovery. Further, these marketable securities were initially, and continue to be, held with investment grade, high credit quality institutions. All marketable securities with unrealized losses as of each balance sheet date have been in a loss position for less than 12 months or the loss is not material.

All of the Company’s marketable securities have an effective maturity of less than two years.

Stock-Based Awards - Summary of Assumptions Used for Estimating the Fair Value of Stock Options Granted (Details) - Stock Options	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected term (in years)	6 years 29 days	6 years 29 days
Volatility, minimum	65.50%	62.20%
Volatility, maximum	66.10%	63.40%
Risk-free interest rate, minimum	1.50%	0.50%
Risk-free interest rate, maximum	1.80%	1.00%
Dividend yield	0.00%	0.00%

Collaboration Agreements

3 Months Ended

Mar. 31, 2022

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaboration Agreements

Biogen

In August 2020, the Company entered into a binding Provisional Collaboration and License Agreement (“Provisional Biogen Collaboration Agreement”) with Biogen Inc.’s subsidiaries, Biogen MA Inc. (“BIMA”) and Biogen International GmbH (“BIG”) (BIMA and BIG, collectively, “Biogen”), which expired in October 2020 upon the execution of a Definitive LRRK2 Collaboration and License Agreement (“LRRK2 Agreement”) with Biogen on October 4, 2020 and a Right of First Negotiation, Option and License Agreement (the “ROFN and Option Agreement”) on October 6, 2020 (collectively, the "Biogen Collaboration Agreement"). The details of the Provisional Biogen Collaboration Agreement and the Biogen Collaboration Agreement and the payments the Company has received, and is entitled to receive, are further described in Note 6, Collaboration Agreements, to the consolidated financial statements in the 2021 Annual Report on Form 10-K. During the first quarter of 2022, there were no changes to the terms of the Company’s collaboration agreement with Biogen, and no change in the transaction price for the Biogen Collaboration Agreement has been recorded during the three months ended March 31, 2022.

A related party contract liability of $291.5 million and $293.7 million was recorded on the Condensed Consolidated Balance Sheets as of March 31, 2022 and December 31, 2021, respectively. Approximately $288.9 million of the March 31, 2022 contract liability relates to the revenue allocated to the material right for an option under the ROFN and Option Agreement which is being deferred until resolution of the option, which is expected to be within one year of the balance sheet date, and $2.6 million of this contract liability relates to the portion of the Option Research Services performance obligation yet to be satisfied, with such amount to be recognized over the estimated period of the services, which is expected to be more than one year. Expenses for cost sharing payments for LRRK2 Development Activities of $2.7 million were recorded as research and development expenses in the Condensed Consolidated Statement of Operations and Comprehensive Loss for the three months ended March 31, 2022, with the same amount recorded as cost sharing payments due to related party on the Condensed Consolidated Balance Sheets as of March 31, 2022. The Company recorded $2.5 million of cost sharing reimbursements for LRRK2 Development Activities as an offset to research and development expenses in the Condensed Consolidated Statement of Operations and Comprehensive Loss for the three months ended March 31, 2021, and $1.2 million was recorded as cost sharing reimbursements due from related party on the Condensed Consolidated Balance Sheets as of December 31, 2021.

As of March 31, 2022, the Company had not achieved any milestones or recorded any product sales under the Biogen Collaboration Agreement.

Sanofi

In October 2018, the Company entered into a Collaboration and License Agreement ("Sanofi Collaboration Agreement") with Genzyme Corporation, a wholly owned subsidiary of Sanofi S.A. ("Sanofi"). The details of the Sanofi Collaboration Agreement and the payments the Company has received, and is entitled to receive, are further described in Note 6, Collaboration Agreements, to the consolidated financial statements in the Company's 2021 Annual Report on Form 10-K. During the first quarter of 2022, there were no changes to the terms of the Company’s collaboration agreement with Sanofi, and the transaction price of the Sanofi Collaboration Agreement did not change during the three months ended March 31, 2022 or 2021.

A contract liability of $3.4 million was recorded on the Condensed Consolidated Balance Sheets as of both March 31, 2022 and December 31, 2021. This contract liability relates to the portion of the Alzheimer's Disease Services performance obligation yet to be satisfied, with such amounts to be recognized over the estimated period of the services, which is expected to be several years. The Company recorded no receivable associated with the Sanofi Collaboration Agreement on the Condensed Consolidated Balance Sheets as of March 31, 2022 and December 31, 2021, respectively. In April 2022, Sanofi commenced dosing in a Phase 2 study of SAR3820/DNL788 in patients with ALS, triggering a $40.0 million milestone which is due in May 2022.

As of March 31, 2022, the Company had earned milestone payments of $25.0 million and had not recorded any product sales under the Sanofi Collaboration Agreement.

Takeda

Takeda Collaboration Agreement

In January 2018, the Company entered into a Collaboration and Option Agreement ("Takeda Collaboration Agreement") with Takeda Pharmaceutical Company Limited ("Takeda"). The details of the Takeda Collaboration Agreement are further described in Note 6, Collaboration Agreements, to the consolidated financial statements in the Company's 2021 Annual Report on Form 10-K. In March 2022, Takeda and the Company agreed to terminate activity on the ATV:Tau program over which Takeda had an option to develop and commercialize jointly with the Company. As a result of this decision, total preclinical milestone payments that Takeda may owe was reduced to $55.0 million, of which $43.0 million has been received as of March 31, 2022.

A contract liability of $27.9 million was recorded on the Condensed Consolidated Balance Sheets as of December 31, 2021 relating to the remaining Tau program services. As a result of the decision to terminate the ATV:Tau program, the performance obligation related to ATV:Tau was considered fully satisfied, and the contract liability was recognized in its entirety within collaboration revenue from customers in the Condensed Consolidated Statement of Operations and Comprehensive Loss for the three months ended March 31, 2022.

The transaction price of the Takeda Collaboration Agreement increased by $12.0 million during the three months ended March 31, 2022, due to a preclinical milestone being unconstrained. This milestone was triggered by the January 2022 approval of the clinical trial application for TAK-594/DNL593 ("PTV:PGRN") by the Medicines and Healthcare products Regulatory Agency in the UK, and the milestone payment was received in February 2022. There was no contract liability or receivable associated with the Takeda Collaboration Agreement on the Condensed Consolidated Balance Sheets as of March 31, 2022, and no receivable as of December 31, 2021. The Company has no remaining performance obligations under the Takeda Collaboration Agreement, and accordingly the $12.0 million was recorded as collaboration revenue from customers in the three months ended March 31, 2022.

PTV:PGRN and ATV:TREM2 Collaboration Agreements

Opt-in by Takeda on the PTV:PGRN and ATV:TREM2 programs represented two new contracts with a customer for accounting purposes (the "PTV:PGRN Collaboration Agreement" and the "ATV:TREM2 Collaboration Agreement"), both effective in December 2021. The details of the PTV:PGRN Collaboration Agreement and the ATV:TREM2 Collaboration Agreement are further described in Note 6, Collaboration Agreements, to the consolidated financial statements in the Company's 2021 Annual Report on Form 10-K.

During the first quarter of 2022, there were no changes to the terms of either the PTV:PGRN Collaboration Agreement or the ATV:TREM2 Collaboration Agreement, and there was no change in the transaction price of either agreement during the three months ended March 31, 2022. Under the PTV:PGRN Collaboration Agreement and the ATV:TREM2 Collaboration Agreement, Takeda may be obligated to pay the Company up to an aggregate of $280.0 million upon achievement of certain clinical milestone events and up to an aggregate of $200.0 million in regulatory milestone events relating to receipt of regulatory approval in the United States, certain European countries and Japan. Takeda may also be obligated to pay the Company up to $75.0 million per biologic product upon achievement of a certain sales-based milestone, or an aggregate of $150.0 million if one biologic product from each program achieves this milestone.

The Company recorded $2.9 million and $2.1 million of cost sharing reimbursements for PTV:PGRN and ATV:TREM2 Development Activities, respectively, as an offset to research and development expenses in the Condensed Consolidated Statement of Operations and Comprehensive Loss for the three months ended March 31, 2022, the entirety of which is also recorded as a receivable within prepaid expenses and other current assets on the Condensed Consolidated Balance Sheet as of March 31, 2022.

As of March 31, 2022, the Company had earned $53.0 million in preclinical milestone and option fee payments from Takeda, and had not recorded any product sales under the Takeda Collaboration Agreement.

Collaboration Revenue

Revenue disaggregated by collaboration agreement and performance obligation is as follows (in thousands):


	Three Months Ended March 31,
	2022		2021
Takeda Collaboration Agreement:
Takeda Collaboration Agreement Services(1)	$	39,916	$	7,030


Total Takeda Collaboration Revenue	39,916		7,030
Sanofi Collaboration Agreement


Alzheimer's Disease Services(2)	—		1

Total Sanofi Collaboration Revenue	—		1
Biogen Collaboration Agreement



Option Research Services(2)	2,225		892
Total Biogen Collaboration Revenue	2,225		892
Total Collaboration Revenue	$	42,141	$	7,923

_________________________________________________

(1)$27.9 million and $5.7 million of revenue for the three months ended March 31, 2022 and March 31, 2021, respectively, was included in the contract liability balance at the beginning of the period.

(2)Revenue for the three months ended March 31, 2022 and March 31, 2021 represent amounts that were included in the contract liability balance at the beginning of the respective period.

Stock-Based Awards (Tables)

3 Months Ended

Mar. 31, 2022

Share-based Payment Arrangement [Abstract]

Summary of Stock Option Activity

The following table summarizes stock option activity for the three months ended March 31, 2022:


	Number of Options	Weighted-Average Exercise Price
Balance at December 31, 2021	13,686,386	$	24.33
Granted	1,830,168	46.67
Exercised	(151,419)	9.66
Forfeited	(67,087)	44.04
Balance at March 31, 2022	15,298,048	$	27.06
Vested and expected to vest at March 31, 2022	13,562,353	$	30.43
Exercisable at March 31, 2022	9,017,879	$	19.19

Summary of Assumptions Used for Estimating the Fair Value of Stock Granted

The estimated fair value of stock options granted to employees were calculated using the Black-Scholes option-pricing model using the following assumptions:


	Three Months Ended March 31,
	2022	2021
Expected term (in years)	6.08	6.08
Volatility	65.5% - 66.1%	62.2% - 63.4%
Risk-free interest rate	1.5% - 1.8%	0.5% - 1.0%
Dividend yield	—	—

Summary of Restricted Stock Activity

The following table summarizes restricted stock unit ("RSU") activity for the three months ended March 31, 2022:


	Number of RSU shares	Weighted-Average Fair Value at Date of Grant per Share
Unvested at December 31, 2021	2,629,980	$	43.97
Granted	779,843	46.55
Vested and released	(423,184)	43.80
Forfeited	(35,140)	45.87
Unvested at March 31, 2022	2,951,499	$	44.65
Expected to vest at March 31, 2022	2,951,499	$	44.65

Summary of Stock-Based Compensation Expense

The Company’s results of operations include expenses relating to stock-based compensation as follows (in thousands):


	Three Months Ended March 31,
	2022		2021
Research and development	$	15,556	$	12,314
General and administrative	10,589		8,714
Total	$	26,145	$	21,028

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2022	Mar. 31, 2021
Operating activities
Net loss	$ (65,220)	$ (70,041)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	2,079	2,108
Stock–based compensation expense	26,145	21,028
Net amortization of premiums on marketable securities	1,627	1,161
Non-cash adjustment to operating lease expense	(783)	(691)
Other non-cash items	0	(2)
Changes in operating assets and liabilities:
Prepaid expenses and other assets	1,242	6,301
Accounts payable	1,248	623
Accruals and other current liabilities	(8,306)	(10,804)
Contract liabilities	(27,915)	969
Related party contract liability	(2,226)	(892)
Net cash used in operating activities	(72,109)	(50,240)
Investing activities
Purchases of marketable securities	(364,337)	(463,105)
Purchases of property and equipment	(4,041)	(2,800)
Maturities and sales of marketable securities	250,500	440,500
Net cash used in investing activities	(117,878)	(25,405)
Financing activities
Proceeds from exercise of awards under equity incentive plans	1,463	3,822
Net cash provided by financing activities	1,463	3,822
Net decrease in cash, cash equivalents and restricted cash	(188,524)	(71,823)
Cash, cash equivalents and restricted cash at beginning of period	294,977	508,644
Cash, cash equivalents and restricted cash at end of period	106,453	436,821
Supplemental disclosures of cash flow information
Property and equipment purchases accrued but not yet paid	$ 114	$ 0

Commitments and Contingencies

3 Months Ended

Mar. 31, 2022

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Lease Obligations

In May 2018, the Company entered into an operating lease for its corporate headquarters in South San Francisco (the "Headquarters Lease"), and in August 2021, the Company entered into an operating lease for laboratory, office and warehouse premises in Salt Lake City, Utah (“SLC Lease”). The details of both leases are further described in Note 9, Commitments and Contingencies, to the consolidated financial statements in the Company's 2021 Annual Report on Form 10-K. During the first quarter of 2022, there were no changes to the terms of either lease. Further, for accounting purposes, the SLC lease has not yet commenced as the landlord has not yet made the underlying asset available for use by Denali, and as such, no lease liability or ROU asset is recorded on the Condensed Consolidated Balance Sheets as of March 31, 2022, and no operating lease expense has been recorded for the three months ended March 31, 2022.

Management exercised judgment in applying the requirements of ASC 842, including the determination as to whether certain contracts contain a lease and for the headquarters lease, the discount rate used to determine the measurement of the lease liability. The discount rate of our headquarters lease is an approximation of the Company's incremental borrowing rate and is dependent upon the term and economics of the agreement. To estimate the incremental borrowing rate, management considered observable debt yields of comparable market instruments, as well as benchmarks within the headquarters lease agreement that may be indicative of the rate implicit in the lease.

The following table contains a summary of the lease costs recognized under ASC 842 and other information pertaining to the Company’s operating lease for the periods presented (in thousands):


	Three Months Ended March 31,
	2022			2021
Operating lease cost (1)	$	2,863		$	2,789
Cash paid for amounts included in measurement of lease liability	$	2,618		$	2,536

	As of March 31,
	2022			2021
Weighted average remaining lease term	7.1 years			8.1 years
Weighted average discount rate	9		%	9		%

__________________________________________________

(1)Including variable and short-term lease costs


Year Ended December 31:
2022 (nine months)	8,084
2023	11,053
2024	11,417
2025	11,793
2026	12,182
Thereafter	29,966
Total undiscounted lease payments	84,495
Present value adjustment	(21,750)
Net operating lease liabilities	$	62,745

Sublease

In October 2018, the Company entered into a sublease agreement ("Sublease Agreement") for space in the corporate headquarters. The details of the Sublease Agreement are further described in Note 9, Commitments and Contingencies, to the consolidated financial statements in the Company's 2021 Annual Report on Form 10-K. During the first quarter of 2022, there were no changes to the terms of the Sublease Agreement. Total sublease income, including rent and variable sublease cost reimbursements, was $1.0 million and $0.9 million for the three months ended March 31, 2022 and 2021, respectively.

The following table details the future undiscounted cash inflows relating to the Sublease Agreement as of March 31, 2022 (in thousands):


Year Ended December 31:
2022 (nine months)	2,272
2023	3,096
2024	876
2025 and thereafter	—
Total undiscounted sublease receipts	$	6,244

Indemnification

In the ordinary course of business, the Company may provide indemnifications of varying scope and terms to vendors, lessors, business partners, board members, officers, and other parties with respect to certain matters, including, but not limited to, losses arising out of breach of such agreements, services to be provided by the Company, negligence or willful misconduct of the Company, violations of law by the Company, or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with directors and certain officers and employees that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors, officers or employees. No demands have been made upon the Company to provide indemnification under such agreements, and thus, there are no claims that the Company is aware of that could have a material effect on the Company’s Condensed Consolidated Balance Sheets, Condensed Consolidated Statements of Operations and Comprehensive Loss, or Condensed Consolidated Statements of Cash Flows.

Commitments

Effective September 2017, the Company entered into a Development and Manufacturing Services Agreement as amended (“DMSA”) with Lonza Sales AG (“Lonza”) for the development and manufacture of biologic products. Under the DMSA, the Company will execute purchase orders based on project plans authorizing Lonza to provide development and manufacturing services with respect to certain of the Company's antibody and enzyme products, and will pay for the services provided and batches delivered in accordance with the DMSA and project plan. Unless earlier terminated, the DMSA will expire on the later of September 6, 2022 or when all development and manufacturing services are completed.

As of March 31, 2022 and December 31, 2021, the Company had open purchase orders for biological product development and manufacturing costs totaling $44.6 million and $35.8 million, respectively. The activities under these purchase orders are expected to be completed by December 2025. As of March 31, 2022 and December 31, 2021, the Company had total non-cancellable purchase commitments under the DMSA of $35.2 million and $28.3 million, respectively.

During the three months ended March 31, 2022 and 2021, the Company incurred costs of $10.0 million and $5.2 million, respectively, and made payments of $8.7 million and $0.7 million, respectively, for the development and manufacturing services rendered under the DMSA.

Contingencies

From time to time, the Company may be involved in lawsuits, arbitration, claims, investigations and proceedings consisting of intellectual property, employment and other matters which arise in the ordinary course of business. The Company records accruals for loss contingencies to the extent that the Company concludes that it is probable that a liability has been incurred and the amount of the related loss can be reasonably estimated.

Net Loss Per Share

3 Months Ended

Mar. 31, 2022

Earnings Per Share [Abstract]

Net Loss Per Share

Since the Company was in a loss position for all periods presented, basic net loss per share is the same as diluted net loss per share for all periods as the inclusion of all potential shares of common stock outstanding would have been anti-dilutive.

Potentially dilutive securities that were not included in the diluted per share calculations because they would be anti-dilutive were as follows:


	Three Months Ended March 31,
	2022	2021
Options issued and outstanding and ESPP shares issuable	15,447,944	14,323,256
Restricted shares subject to future vesting	2,951,499	2,699,107

Total	18,399,443	17,022,363

Derivative Financial Instruments

3 Months Ended

Mar. 31, 2022

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Derivative Financial Instruments

Foreign Currency Exchange Rate Exposure

The Company uses forward foreign currency exchange contracts to hedge certain operational exposures resulting from potential changes in foreign currency exchange rates. Such exposures result from portions of the Company’s forecasted cash flows being denominated in currencies other than the U.S. dollar, primarily the Euro and British Pound. The derivative instruments the Company uses to hedge this exposure are not designated as cash flow hedges, and as a result, changes in their fair value are recorded in interest and other income, net, on the Company's Condensed Consolidated Statements of Operations and Comprehensive Loss.

The fair values of forward foreign currency exchange contracts are estimated using current exchange rates and interest rates and take into consideration the current creditworthiness of the counterparties. Information regarding the specific instruments used by the Company to hedge its exposure to foreign currency exchange rate fluctuations is provided below.

The following table summarizes the Company’s forward foreign currency exchange contracts outstanding as of March 31, 2022 and December 31, 2021, respectively (notional amounts in thousands):


Foreign Exchange Contracts	Number of Contracts	Aggregate Notional(1) Amount in Foreign Currency	Maturity
Euros	3	150	Apr 2022 - Jun 2022
British Pounds	3	300	Apr 2022 - Jun 2022
Total at March 31, 2022	6
Euros	7	800	Jan 2022 - Jun 2022
British Pounds	6	900	Jan 2022 - Jun 2022
Total at December 31, 2021	13

_________________________________________________

(1) The notional amount represents the net amount of foreign currency that will be received upon maturity of the forward contracts.

Net Loss Per Share (Tables)

3 Months Ended

Mar. 31, 2022

Earnings Per Share [Abstract]

Schedule of Dilutive Securities Not Included in Diluted Per Share Calculations

Potentially dilutive securities that were not included in the diluted per share calculations because they would be anti-dilutive were as follows:


	Three Months Ended March 31,
	2022	2021
Options issued and outstanding and ESPP shares issuable	15,447,944	14,323,256
Restricted shares subject to future vesting	2,951,499	2,699,107

Total	18,399,443	17,022,363

Marketable Securities (Tables)

3 Months Ended

Mar. 31, 2022

Investments, Debt and Equity Securities [Abstract]

Summary of Available for Sale Securities

The amortized cost, gross unrealized holding gains or losses, and fair value of the Company’s marketable securities by major security type at each balance sheet date are summarized in the tables below (in thousands):


	March 31, 2022
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries(1)	$	703,031	$	—	$	(3,735)	$	699,296

Corporate debt securities(2)	72,422		—		(281)		72,141
Commercial paper	81,132		—		—		81,132
Total short-term marketable securities	856,585		—		(4,016)		852,569
Long-term marketable securities:
U.S. government treasuries(3)	227,708		—		(4,653)		223,055

Corporate debt securities(4)	27,443		—		(230)		27,213
Total long-term marketable securities	255,151		—		(4,883)		250,268
Total	$	1,111,736	$	—	$	(8,899)	$	1,102,837

__________________________________________________

(1)Unrealized holding losses on 43 securities with an aggregate fair value of $699.3 million.

(2)Unrealized holding losses on 19 securities with an aggregate fair value of $68.6 million.

(3)Unrealized holding losses on 18 securities with an aggregate fair value of $223.1 million.

(4)Unrealized holding losses on 5 securities with an aggregate fair value of $27.2 million.


	December 31, 2021
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries(1)	$	450,689	$	—	$	(253)	$	450,436

Corporate debt securities(2)	70,076		1		(68)		70,009
Commercial paper	51,485		—		—		51,485
Total short-term marketable securities	572,250		1		(321)		571,930
Long-term marketable securities:
U.S. government treasuries(3)	411,904		—		(1,757)		410,147

Corporate debt securities(4)	15,373		—		(71)		15,302
Total long-term marketable securities	427,277		—		(1,828)		425,449
Total	$	999,527	$	1	$	(2,149)	$	997,379

__________________________________________________

(1)Unrealized holding losses on 19 securities with an aggregate fair value of $450.4 million.

(2)Unrealized holding losses on 16 securities with an aggregate fair value of $68.5 million.

(3)Unrealized holding losses on 16 securities with an aggregate fair value of $410.1 million.

(4)Unrealized holding losses on 6 security with an aggregate fair value of $15.3 million.

Collaboration Agreements - Biogen (Details)

3 Months Ended

Mar. 31, 2022

USD ($)

milestone

Mar. 31, 2021

USD ($)

Dec. 31, 2021

USD ($)

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Research and development expense

^[1]

$ 86,098,000

$ 60,207,000

Cost sharing payments due to related party

2,713,000

$ 0

Cost sharing reimbursements due from related party

1,226,000

Biogen Collaboration Agreement | Related Party

^[2]

42,141,000

7,922,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Biogen Collaborative Arrangement | Biogen Collaboration Agreement

291,500,000

293,700,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Research and development expense

2,700,000

Offset to research and development expense, related party cost reimbursement

$ 2,500,000

Cost sharing payments due to related party

$ 2,700,000

Cost sharing reimbursements due from related party

$ 1,200,000

Number of milestones achieved | milestone

Biogen Collaborative Arrangement | Biogen Collaboration Agreement | Option Research Services | Related Party

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Biogen Collaborative Arrangement | Biogen Collaboration Agreement | Option Research Services | Related Party | Minimum

$ 2,600,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Performance obligation, period

one year

Biogen Collaborative Arrangement | Biogen Collaboration Agreement | Product

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

ROFN and Option Agreement | Biogen Collaboration Agreement | Related Party

$ 0

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

ROFN and Option Agreement | Biogen Collaboration Agreement | Material Right For An Option | Related Party | Maximum

$ 288,900,000

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Performance obligation, period

one year

[1]	Includes expense for cost sharing payments to a related party of $2.7 million for the three months ended March 31, 2022, and an offset to expense from related party cost sharing reimbursements of $2.5 million for the three months ended March 31, 2021.
[2]	Includes related party collaboration revenue from a customer of $2.2 million and $0.9 million for the three months ended March 31, 2022 and 2021, respectively.

Stock-Based Awards - Summary of Restricted Stock Activity (Details) - Restricted Stock Units (RSUs)	3 Months Ended
	Mar. 31, 2022 $ / shares shares
Number of RSU shares
Beginning balance (in shares) \| shares	2,629,980
Granted (in shares) \| shares	779,843
Vested and released (in shares) \| shares	(423,184)
Forfeited (in shares) \| shares	(35,140)
Ending balance (in shares) \| shares	2,951,499
Expected to vest (in shares) \| shares	2,951,499
Weighted-Average Fair Value at Date of Grant per Share
Beginning balance (usd per share) \| $ / shares	$ 43.97
Granted (usd per share) \| $ / shares	46.55
Vested and released (usd per share) \| $ / shares	43.80
Forfeited (usd per share) \| $ / shares	45.87
Ending balance (usd per share) \| $ / shares	44.65
Expected to vest (usd per share) \| $ / shares	$ 44.65

Fair Value Measurements

3 Months Ended

Mar. 31, 2022

Fair Value Disclosures [Abstract]

Fair Value Measurements

Assets and liabilities measured at fair value at each balance sheet date are as follows (in thousands):


	March 31, 2022
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	53,888	$	—	$	—	$	53,888
U.S. government treasuries	10,013		—		—		10,013
Commercial paper	—		29,985		—		29,985
Short-term marketable securities:
U.S. government treasuries	699,296		—		—		699,296

Corporate debt securities	—		72,141		—		72,141
Commercial paper	—		81,132		—		81,132
Long-term marketable securities:
U.S. government treasuries	223,055		—		—		223,055

Corporate debt securities	—		27,213		—		27,213

Total	$	986,252	$	210,471	$	—	$	1,196,723
Liabilities:
Foreign currency derivative contracts	$	—	$	44	$	—	$	44
Total	$	—	$	44	$	—	$	44


	December 31, 2021
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	265,294	$	—	$	—	$	265,294

Short-term marketable securities:
U.S. government treasuries	450,436		—		—		450,436

Corporate debt securities	—		70,009		—		70,009
Commercial paper	—		51,485		—		51,485
Long-term marketable securities:
U.S. government treasuries	410,147		—		—		410,147
Corporate debt securities	—		15,302		—		15,302

Total	$	1,125,877	$	136,796	$	—	$	1,262,673
Liabilities:
Foreign currency derivative contracts	$	—	$	111	$	—	$	111
Total	$	—	$	111	$	—	$	111

The carrying amounts of prepaid expenses and other current assets, accounts payable, cost sharing payments due to or from a related party and accrued liabilities approximate their fair values due to their short-term maturities.

The Company’s Level 2 securities are valued using third-party pricing sources. The pricing services utilize industry standard valuation models, including both income and market-based approaches, for which all significant inputs are observable, either directly or indirectly.

The Company has not transferred any assets or liabilities between the fair value measurement levels.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($)
$ in Thousands

3 Months Ended

Mar. 31, 2022

Mar. 31, 2021

Collaboration revenue:

Other collaboration revenue

^[1]

$ 42,141

$ 7,922

Total collaboration revenue

42,141

7,923

Operating expenses:

Research and development

^[2]

86,098

60,207

General and administrative

22,541

18,936

Total operating expenses

108,639

79,143

Loss from operations

(66,498)

(71,220)

Interest and other income, net

1,278

1,179

Net loss

(65,220)

(70,041)

Other comprehensive income (loss):

Net unrealized gain (loss) on marketable securities, net of tax

(6,752)

Comprehensive loss

$ (71,972)

$ (70,028)

Net loss per share, basic (usd per share)

$ (0.53)

$ (0.58)

Net loss per share, diluted (usd per share)

$ (0.53)

$ (0.58)

Weighted average number of shares outstanding, basic (in shares)

122,673,935

120,884,665

Weighted average number of shares outstanding, diluted (in shares)

122,673,935

120,884,665

[1]	Includes related party collaboration revenue from a customer of $2.2 million and $0.9 million for the three months ended March 31, 2022 and 2021, respectively.
[2]	Includes expense for cost sharing payments to a related party of $2.7 million for the three months ended March 31, 2022, and an offset to expense from related party cost sharing reimbursements of $2.5 million for the three months ended March 31, 2021.

Collaboration Agreements (Tables)

3 Months Ended

Mar. 31, 2022

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Summary of Collaboration Revenue

Revenue disaggregated by collaboration agreement and performance obligation is as follows (in thousands):


	Three Months Ended March 31,
	2022		2021
Takeda Collaboration Agreement:
Takeda Collaboration Agreement Services(1)	$	39,916	$	7,030


Total Takeda Collaboration Revenue	39,916		7,030
Sanofi Collaboration Agreement


Alzheimer's Disease Services(2)	—		1

Total Sanofi Collaboration Revenue	—		1
Biogen Collaboration Agreement



Option Research Services(2)	2,225		892
Total Biogen Collaboration Revenue	2,225		892
Total Collaboration Revenue	$	42,141	$	7,923

_________________________________________________

(1)$27.9 million and $5.7 million of revenue for the three months ended March 31, 2022 and March 31, 2021, respectively, was included in the contract liability balance at the beginning of the period.

(2)Revenue for the three months ended March 31, 2022 and March 31, 2021 represent amounts that were included in the contract liability balance at the beginning of the respective period.

Collaboration Agreements - Summary of Collaboration Revenue (Details) - USD ($)
$ in Thousands

3 Months Ended

Mar. 31, 2022

Mar. 31, 2021

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative revenue, revenue from contract with customer

^[1]

$ 42,141

$ 7,922

Collaborative revenue, excluding revenue from contract with customer

Takeda Collaboration Agreement

42,141

7,923

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenue recognized included in the contract liability balance at the beginning of the period

39,916

7,030

27,900

5,700

Takeda Collaboration Agreement | Collaboration Agreement Services

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative revenue, revenue from contract with customer

39,916

7,030

Sanofi Collaboration Agreement

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Sanofi Collaboration Agreement | Alzheimer's Disease Services

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative revenue, excluding revenue from contract with customer

Biogen Collaboration Agreement

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]