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

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 ☒ No ☐

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 ☒ No ☐

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

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. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

The number of shares of the registrant’s common stock outstanding as of ~~April 30, 2021~~January 31, 2022 was ~~104,084,876.~~105,459,716.

	(unaudited) March 31, 2021			September 30, 2020			(unaudited) December 31, 2021			September 30, 2021
ASSETS
CURRENT ASSETS
Cash and cash equivalents	$	372,377		$	143,583		$	91,587		$	184,434
Accounts receivable		955			845			150			10,255
Prepaid expenses		6,639			4,250			5,199			4,362
Other current assets		1,845			1,782			2,795			2,191
Marketable securities		125,793			85,020			126,010			126,728
Short term investments (held to maturity)		79,148			86,890
Short term investments								112,537			56,627
TOTAL CURRENT ASSETS		586,757			322,370			338,278			384,597
Property and equipment, net		39,400			30,881			52,303			48,675
Intangible assets, net		14,513			15,363			13,238			13,663
Long term investments (held to maturity)		97,490			137,487
Long term investments								217,572			245,595
Right-of-use assets		18,370			16,138			16,875			17,346
Other assets		265			265			273			272
TOTAL ASSETS	$	756,795		$	522,504		$	638,539		$	710,148
LIABILITIES AND STOCKHOLDERS’ EQUITY
CURRENT LIABILITIES
Accounts payable	$	5,299		$	6,829		$	4,068		$	9,457
Accrued expenses		12,862			5,389			18,518			14,001
Accrued payroll and benefits		2,859			8,061			2,968			9,773
Lease liabilities		1,272			1,095			2,826			2,250
Deferred revenue		144,879			19,291			108,652			111,055
Other current liabilities		17			16
TOTAL CURRENT LIABILITIES		167,188			40,681			137,032			146,536
LONG-TERM LIABILITIES
Lease liabilities, net of current portion		22,528			20,044			22,489			23,295
Deferred revenue, net of current portion		121,530			-			106,458			131,495
TOTAL LONG-TERM LIABILITIES		144,058			20,044			128,947			154,790
Commitments and contingencies (Note 7)
STOCKHOLDERS’ EQUITY
Arrowhead Pharmaceuticals, Inc. stockholders’ equity:
Common stock, $0.001 par value; 145,000 shares authorized; 104,020 and 102,376 shares issued and outstanding as of March 31, 2021 and September 30, 2020, respectively		196			195
Common stock, $0.001 par value; 145,000 shares authorized; 104,798 and 104,327 shares issued and outstanding as of December 31, 2021 and September 30, 2021, respectively								197			197
Additional paid-in capital		996,645			965,410			1,080,035			1,053,386
Accumulated other comprehensive income		102			18			(108	)		(69	)
Accumulated deficit		(551,394	)		(503,844	)		(707,564	)		(644,692	)
TOTAL STOCKHOLDERS’ EQUITY		445,549			461,779			372,560			408,822
TOTAL LIABILITIES AND STOCKHOLDERS’ EQUITY	$	756,795		$	522,504		$	638,539		$	710,148

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

	Three Months Ended March 31,						Six Months Ended March 31,						Three Months Ended December 31,
	2021			2020			2021			2020			2021			2020
REVENUE	$	32,811		$	23,529		$	54,113		$	52,983		$	27,439		$	21,303
OPERATING EXPENSES
Research and development		44,697			29,443			81,251			52,817			65,765			36,555
General and administrative expenses		16,346			16,326			25,147			27,260			24,995			8,802
TOTAL OPERATING EXPENSES		61,043			45,769			106,398			80,077			90,760			45,357
OPERATING INCOME (LOSS)		(28,232	)		(22,240	)		(52,285	)		(27,094	)		(63,321	)		(24,054	)
OTHER INCOME (EXPENSE)
Interest income, net		1,524			2,404			3,692			4,585			1,156			2,169
Other income (expense)		(110	)		-			1,043			-			(707	)		1,153
TOTAL OTHER INCOME (EXPENSE)		1,414			2,404			4,735			4,585			449			3,322
INCOME (LOSS) BEFORE INCOME TAXES		(26,818	)		(19,836	)		(47,550	)		(22,509	)		(62,872	)		(20,732	)
Provision for income taxes		-			-			-			-			-			-
NET INCOME (LOSS)		(26,818	)		(19,836	)		(47,550	)		(22,509	)		(62,872	)		(20,732	)
NET INCOME (LOSS) PER SHARE - BASIC	$	(0.26	)	$	(0.20	)	$	(0.46	)	$	(0.23	)	$	(0.60	)	$	(0.20	)
NET INCOME (LOSS) PER SHARE - DILUTED	$	(0.26	)	$	(0.20	)	$	(0.46	)	$	(0.23	)	$	(0.60	)	$	(0.20	)
Weighted average shares outstanding - basic		103,867			101,653			103,303			99,359			104,534			102,757
Weighted average shares outstanding - diluted		103,867			101,653			103,303			99,359			104,534			102,757
OTHER COMPREHENSIVE INCOME (LOSS), NET OF TAX:
Foreign currency translation adjustments		(96	)		(433	)		84			(238	)		(39	)		180
COMPREHENSIVE INCOME (LOSS)	$	(26,914	)	$	(20,269	)	$	(47,466	)	$	(22,747	)	$	(62,911	)	$	(20,552	)

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

	Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals
Balance at December 31, 2019		101,112	$	193	$	922,051		$	(196	)	$	(421,964	)	$	(555	)	$	499,529
Stock-based compensation		-		-		12,972			-			-			-			12,972
Exercise of stock options		214		-		1,330			-			-			-			1,330
Common stock - restricted stock units vesting		422		1		(1	)		-			-			-			-
Common stock - issued for cash		-		-		2			-			-			-			2
Foreign currency translation adjustments		-		-		-			(433	)		-			-			(433	)
Net income (loss) for the three months ended March 31, 2020		-		-		-			-			(19,836	)		-			(19,836	)
Balance at March 31, 2020		101,748	$	194	$	936,354		$	(629	)	$	(441,800	)	$	(555	)	$	493,564

	Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Totals
Balance at December 31, 2020		103,194	$	195	$	978,655		$	198		$	(524,576	)	$	454,472
Stock-based compensation		-		-		15,359			-			-			15,359
Exercise of stock options		282		-		2,632			-			-			2,632
Common stock - restricted stock units vesting		544		1		(1	)		-			-			-
Foreign currency translation adjustments		-		-		-			(96	)		-			(96	)
Net income (loss) for the three months ended March 31, 2021		-		-		-			-			(26,818	)		(26,818	)
Balance at March 31, 2021		104,020	$	196	$	996,645		$	102		$	(551,394	)	$	445,549

	Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals
Balance at September 30, 2019		95,506	$	187	$	664,086		$	(391	)	$	(419,291	)	$	(555	)	$	244,036
Stock-based compensation		-		-		17,464			-			-			-			17,464
Exercise of stock options		686		1		4,331			-			-			-			4,332
Common stock - restricted stock units vesting		956		1		(1	)		-			-			-			-
Common stock - issued for cash		4,600		5		250,474			-			-			-			250,479
Foreign currency translation adjustments		-		-		-			(238	)		-			-			(238	)
Net income (loss) for the six months ended March 31, 2020		-		-		-			-			(22,509	)		-			(22,509	)
Balance at March 31, 2020		101,748	$	194	$	936,354		$	(629	)	$	(441,800	)	$	(555	)	$	493,564

	Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Totals						Common Stock		Amount ($)		Additional Paid-In Capital		Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Totals
Balance at September 30, 2020		102,376	$	195	$	965,410		$	18		$	(503,844	)	$	461,779						102,376	$	195	$	965,410	$	18		$	(503,844	)	$	461,779
Stock-based compensation		-		-		23,502			-			-			23,502						-		-		8,144		-			-			8,144
Exercise of stock options		820		-		7,734			-			-			7,734						538		-		5,101		-			-			5,101
Common stock - restricted stock units vesting		824		1		(1	)		-			-			-						280		-		-		-			-			-
Foreign currency translation adjustments		-		-		-			84			-			84						-		-		-		180			-			180
Net income (loss) for the six months ended March 31, 2021		-		-		-			-			(47,550	)		(47,550	)
Balance at March 31, 2021		104,020	$	196	$	996,645		$	102		$	(551,394	)	$	445,549
Net income (loss) for the three months ended December 31, 2020																					-		-		-		-			(20,732	)		(20,732	)
Balance at December 31, 2020																					103,194	$	195	$	978,655	$	198		$	(524,576	)	$	454,472

																				Common Stock		Amount ($)		Additional Paid-In Capital		Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Totals
Balance at September 30, 2021																					104,327	$	197	$	1,053,386	$	(69	)	$	(644,692	)	$	408,822
Stock-based compensation																					-		-		24,504		-			-			24,504
Exercise of stock options																					208				2,145		-			-			2,145
Common stock - restricted stock units vesting																					263		-		-		-			-			-
Foreign currency translation adjustments																					-		-		-		(39	)		-			(39	)
Net income (loss) for the three months ended December 31, 2021																					-		-		-		-			(62,872	)		(62,872	)
Balance at December 31, 2021																					104,798	$	197	$	1,080,035	$	(108	)	$	(707,564	)	$	372,560

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

	Six Months Ended March 31,						Three Months Ended December 31,
	2021			2020			2021			2020
CASH FLOWS FROM OPERATING ACTIVITIES:
Net income (loss)	$	(47,550	)	$	(22,509	)	$	(62,872	)	$	(20,732	)
Stock-based compensation		23,502			17,464			24,504			8,144
Depreciation and amortization		3,766			2,632			2,573			1,848
Amortization/(accretion) of note premiums/discounts		193			419			(280	)		(302	)
Changes in operating assets and liabilities:
Accounts receivable		(109	)		(604	)		10,105			(8,157	)
Prepaid expenses and other current assets		(2,213	)		47			(1,181	)		(3,193	)
Deferred revenue		247,118			(49,630	)		(27,439	)		(12,547	)
Accounts payable		(1,530	)		5,768			(5,389	)		(2,002	)
Accrued expenses		2,271			(5,425	)		(2,290	)		(1,126	)
Other		(497	)		723			922			(855	)
NET CASH PROVIDED BY (USED IN) OPERATING ACTIVITIES		224,951			(51,115	)		(61,347	)		(38,922	)
CASH FLOWS FROM INVESTING ACTIVITIES:
Purchases of property and equipment		(11,437	)		(7,929	)		(5,778	)		(4,271	)
Purchases of investments		(40,000	)		(180,523	)		(65,875	)		-
Proceeds from sale of investments		47,545			19,603			38,268			34,429
NET CASH PROVIDED BY (USED IN) INVESTING ACTIVITIES		(3,892	)		(168,849	)		(33,385	)		30,158
CASH FLOWS FROM FINANCING ACTIVITIES:
Proceeds from the exercises of stock options		7,735			4,332			1,885			5,102
Proceeds from the issuance of common stock		-			250,479
NET CASH PROVIDED BY (USED IN) FINANCING ACTIVITIES		7,735			254,811			1,885			5,102
NET INCREASE (DECREASE) IN CASH		228,794			34,847			(92,847	)		(3,662	)
CASH AND CASH EQUIVALENTS AT BEGINNING OF PERIOD		143,583			221,804			184,434			143,583
CASH AND CASH EQUIVALENTS AT END OF PERIOD	$	372,377		$	256,651		$	91,587		$	139,921

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

Unless otherwise noted, (1) the term “Arrowhead” refers to Arrowhead Pharmaceuticals, Inc., a Delaware corporation and its Subsidiaries, (2) the terms “Company,” “we,” “us,” and “our,” refer to the ongoing business operations of Arrowhead and its Subsidiaries, whether conducted through Arrowhead or a subsidiary of Arrowhead, (3) the term “Subsidiaries” refers to Arrowhead Madison Inc. (“Arrowhead Madison”) and Arrowhead Australia Pty Ltd (“Arrowhead Australia”), (4) the term “Common Stock” refers to Arrowhead’s Common Stock, par value $0.001 per share, (5) the term “Preferred Stock” refers to Arrowhead’s Preferred Stock, par value $0.001 per share, and (6) the term “Stockholder(s)” refers to the holders of ~~Arrowhead~~Arrowhead’s Common Stock.

Arrowhead Pharmaceuticals, Inc. develops medicines that treat intractable diseases by silencing the genes that cause them. Using a broad portfolio of RNA chemistries and efficient modes of delivery, Arrowhead therapies trigger the RNA interference mechanism to induce rapid, deep and durable knockdown of target genes. RNA interference (“RNAi”) is a mechanism present in living cells that inhibits the expression of a specific gene, thereby affecting the production of a specific protein. Arrowhead’s RNAi-based therapeutics leverage this natural pathway of gene silencing. The Company’s pipeline includes ARO-APOC3 for hypertriglyceridemia, ARO-ANG3 for dyslipidemia, ~~ARO-HSD for liver disease,~~ ARO-ENaC for cystic fibrosis, ARO-HIF2 for renal cell carcinoma, ARO-DUX4 for facioscapulohumeral muscular dystrophy, ~~ARO-LUNG2~~ARO-LUNG2 for chronic obstructive pulmonary disorder, ~~(“COPD”), and~~ ARO-COV for the coronavirus that causes COVID-19 and other possible future pulmonary-borne ~~pathogens.~~pathogens, ARO-C3 for complement mediated diseases and ARO-RAGE and ARO-MUC5AC for various muco-obstructive or inflammatory pulmonary conditions. ARO-HSD for liver disease was out-licensed to Glaxosmithkline Intellectual Property (No. 3) Limited ~~ARO-JNJ1,~~(“GSK”) in November 2021. ARO-XDH is being developed for uncontrolled gout under a collaboration agreement with Horizon Therapeutics Ireland DAC (“Horizon”). ARO-JNJ2 and ARO-JNJ3 are being developed for undisclosed liver-expressed targets under a collaboration agreement with Janssen Pharmaceuticals, Inc. (“Janssen”). JNJ-75220795 (ARO-JNJ1) is being developed by Janssen as a potential treatment for patients with non-alcoholic steatohepatitis (NASH). ARO-AAT for liver disease associated with alpha-1 antitrypsin deficiency (“AATD”) was out-licensed to Takeda Pharmaceuticals U.S.A., Inc. (“Takeda”) in October 2020. ~~JNJ3989~~JNJ-3989 (formerly referred to as ARO-HBV) for chronic hepatitis B virus was out-licensed to Janssen in October 2018. Olpasiran (formerly referred to as AMG 890 or ARO-LPA) for cardiovascular disease was out-licensed to Amgen Inc. (“Amgen”) in 2016.

Arrowhead operates lab facilities in Madison, Wisconsin and San Diego, California, where the Company’s research and development activities, including the development of RNAi therapeutics, take place. The Company’s principal executive offices are located in Pasadena, ~~California.~~California.

During the first ~~half~~quarter of fiscal ~~year 2021,~~2022, the Company continued to develop and advance its pipeline and partnered ~~candidates. The Company hosted a key opinion leader webinar on~~candidates and expanded its ~~cardiometabolic candidates, ARO-APOC3 and ARO-ANG3. The Company presented positive interim clinical data from AROAAT2002, an open-label Phase 2 clinical study of ARO-AAT,~~facilities to support the Company’s second-generation investigational RNAi therapeutic being developed as a treatment for the rare genetic liver disease associated with AATD. The Company also announced positive clinical data on its cardiometabolic candidates, ARO-APOC3 and ARO-ANG3, at the American Heart Association Scientific Sessions 2020. The Company filed two Investigational New Drug Applications with the United States Food and Drug Administration to begin a Phase 2b clinical study of ARO-APOC3 in patients with severe hypertriglyceridemia and a Phase 2b clinical study of ARO-ANG3 in patients with mixed dyslipidemia. Finally, the Company announced a collaboration with Takeda to co-develop and co-commercialize ARO-AAT for alpha-1 antitrypsin-associated liver disease. See Note 2 for more information regarding the collaboration with Takeda.growing pipeline. Several key recent developments include:

~~The Company’s~~ partnered candidates under its collaboration agreements also continued to progress. Janssen began dosing patients in a Phase 2b triple combination study called REEF-1, designed to enroll up to 450 patients with chronic hepatitis B infection. In connection with the start of this study, Arrowhead earned a $25.0 million milestone payment under the Company’s License Agreement with Janssen (“Janssen License Agreement”). The Company is currently performing discovery, optimization and preclinical research and development for ARO-JNJ1, ARO-JNJ2 and ARO-JNJ3 for Janssen as part of the Company’s Research Collaboration and Option Agreement with Janssen (“Janssen Collaboration Agreement”). Under the terms of the Janssen agreements taken together, the Company has received $175.0 million as an upfront payment, $75.0 million in the form of an equity investment by Johnson & Johnson Innovation-JJDC, Inc. (“JJDC”) in Arrowhead Common Stock, two $25.0 million milestone payments and may receive up to $1.6 billion in development and sales milestones payments for the Janssen License Agreement, and up to $1.9 billion in development and sales milestone payments for the 3 additional targets covered under the Janssen Collaboration Agreement. The Company is further eligible to receive tiered royalties on product sales up to mid-teens under the Janssen License Agreement and up to low teens under the Janssen Collaboration Agreement.

~~The Company’s collaboration agreement with Amgen for~~ ~~Olpasiran (previously referred to as AMG 890 or ARO-LPA) (the “Second Collaboration and License Agreement” or “Olpasiran Agreement”)~~ ~~continues to progress.~~ ~~In July 2020, Amgen initiated a Phase 2 clinical study, which resulted in a $20.0 million milestone payment to the Company.~~ The Company has received $35.0 million in upfront payments, $21.5 million in the form of an equity investment by Amgen in the Company’s Common Stock, $30.0 million in milestone payments, and may receive up to an additional $400.0 million in remaining development, regulatory and sales

~~milestone payments. The Company is eligible to receive up to low double-digit royalties for sales of products under the~~ ~~Olpasiran~~ ~~Agreement.~~

~~On October 7, 2020, the Company entered into an Exclusive License and Co-Funding Agreement with Takeda (the “Takeda License Agreement”). Under the Takeda License Agreement,~~ Takeda and the Company will co-develop the Company’s ARO-AAT program. Within the United States, ARO-AAT, if approved, will be co-commercialized under a 50/50 profit sharing structure. Outside the United States, Takeda will lead the global commercialization strategy and receive an exclusive license to commercialize ARO-AAT with the Company eligible to receive tiered royalties of 20% to 25% on net sales. In January 2021, the Company received $300.0 million as an upfront payment and is eligible to receive potential development, regulatory and commercial milestones of up to $740.0 million.

~~The revenue recognition for these collaboration agreements is discussed further in Note 2 below.~~

The Company is actively monitoring the ongoing COVID-19 pandemic. The financial results for the three ~~and six~~ months ended ~~March~~December 31, 2021 were not significantly impacted by COVID-19. ~~During fiscal year 2020,~~Operationally, the Company ~~had temporarily paused~~has experienced delays in its earlier stage programs due to a shortage in non-human primates, which are critical to the Company’s preclinical programs. Additionally, the Company has experienced delays in enrollment in its two ARO-AAT studies, SEQUOIA and the ARO-AAT 2002 study, but resumed the process of screening and enrolling patients. During the pause in enrollment, patients already enrolled in these studies continued to be dosed per protocol and continued to come in for their follow up visits. Additional delays have occurred in the Company’s earlier stage programs, but the Company does not expect a material impact to any program’s anticipated timelines. Additionally, theclinical trials. The Company’s operations at its research and development facilities in Madison, Wisconsin and San Diego, California, and its corporate headquarters in Pasadena, California have continued ~~to operate~~ with limited impact, other than for enhanced safety measures, including work from home ~~policies.~~policies and intermittent lab supply shortages. However, the Company cannot predict the impact the progression of COVID-19 will have on future financial and operational results due to a variety of factors, including the ability of the Company’s clinical sites to continue to enroll subjects, the ability of the Company’s suppliers to continue to operate, the continued good health and safety of the Company’s employees and ~~ultimately~~ the length and severity of the COVID-19 pandemic.

The Consolidated Financial Statements have been prepared in conformity with the accounting principles generally accepted in the United States of America (“GAAP”), which contemplate the continuation of the Company as a going concern. Historically, the Company’s primary sources of financing have been through the sale of its securities and revenue from its licensing and collaboration agreements. Research and development activities have required significant capital investment since the Company’s ~~inception. The Company expects its operations~~inception and are expected to continue to require significant cash expenditure in the future, particularly as the Company’s pipeline of drug candidates and its headcount have both expanded significantly. Additionally, significant capital investment ~~to pursue its research and development goals, including~~will be required as the Company’s pipeline matures into later stage clinical trials, ~~and related drug manufacturing.~~as well as with the Company’s plans to increase its internal manufacturing capabilities.

At ~~March~~December 31, 2021, the Company had ~~$372.4~~$91.6 million in cash and cash equivalents (including ~~$2.4~~$3.0 million in restricted cash), ~~$79.1~~$112.5 million in short-term investments, ~~$125.8~~$126.0 million in marketable securities and ~~$97.5~~$217.6 million in long-term investments to fund operations. During the ~~six~~three months ended ~~March~~December 31, 2021, the Company’s cash and investments balance ~~increased~~decreased by ~~$221.8~~$65.7 million, which was primarily ~~the result of the $300 million upfront payment from the Takeda License Agreement, partially offset by~~due to cash being used to fund the Company’s ~~research~~operations.

In total, the Company remains eligible for $6.2 billion in developmental, regulatory and ~~development operations~~sales milestones and ~~general~~various royalties on net sales from its licensing and ~~administrative expenses.~~collaboration agreements. The revenue recognition for these collaboration agreements is discussed further in Note 2 below.

There have been no changes to the significant accounting policies disclosed in the Company’s most recent Annual Report on Form 10-K.

In November 2018, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) No. 2018-18 Collaborative Arrangements (Topic 808). This update provides clarificationThere have been no recent accounting pronouncements that have significantly impacted this Quarterly Report on the interaction between Revenue Recognition (Topic 606) and Collaborative Arrangements (Topic 808) including the alignment of unit of account guidance between the two topics. ASU 2018-18 became effective for the Company on October 1, 2020 and did not have a material impact on its Consolidated Financial Statements.

In August 2018, the FASB issued ASU No. 2018-15 Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract. The new standard requires that certain implementation costs for cloud computing arrangements are capitalized and amortized over the term of the associated hosted cloud computing arrangement service. Capitalized implementation costs are classified in prepaid expenses and other assets. The amortization of the capitalized asset is presentedForm 10-Q, beyond those disclosed in the ~~same line~~Company’s most recent Annual Report on the statement of operations and comprehensive loss as the fees for the associated hosted cloud computing arrangement service and not included with depreciation or amortization expense related to property and equipment or intangible assets. Cash flows related to capitalized implementation costs are presented in cash flows used in operating activities. ASU 2018-15 became effective for the Company on October 1, 2020 and did not have a material impact on its Consolidated Financial Statements. Form 10-K.

On September 28, 2016, the Company entered into 2 collaboration and license agreements and a common stock purchase agreement with Amgen. Under the Second Collaboration and License Agreement ~~or Olpasiran Agreement,~~(the “Olpasiran Agreement”), Amgen has received a worldwide, exclusive license to Arrowhead’s novel RNAi Olpasiran (previously referred to as AMG 890 or ARO-LPA) program. These RNAi molecules are designed to reduce elevated lipoprotein(a), which is a genetically validated, independent risk factor for atherosclerotic cardiovascular disease. Under the ~~other~~prior collaboration and license agreement (the “First Collaboration and License Agreement” or the “ARO-AMG1 Agreement”), Amgen received an option to a worldwide, exclusive license for ARO-AMG1, an RNAi therapy for an undisclosed genetically validated cardiovascular target. InUnder both agreements, Amgen is wholly responsible for clinical development and commercialization. Under the terms of the agreements taken together, the Company has received $35.0 million in upfront payments, $21.5 million in the form of an equity investment by Amgen in the Company’s Common Stock, and $30.0 million in milestone payments, and may receive up to an additional $400.0 million in remaining development, regulatory and sales milestone payments. The Company is further eligible to receive up to low double-digit royalties for sales of products under the Olpasiran Agreement. In July 2019, Amgen informed the Company that it would not be exercising its option for an exclusive license for ARO-AMG1, and as such, there will be no further milestone or royalty payments under the ARO-AMG1 Agreement.

The Company has evaluated these agreements in accordance with FASB Topics 808 – Collaboration Arrangements and 606 - Revenue for Contracts from Customers. The Company has substantially completed its performance obligations under the Olpasiran Agreement and the ARO-AMG1 Agreement. Future milestones and royalties achieved will be recognized in their entirety when earned. In July 2020, Amgen initiated a Phase 2 clinical study of Olpasiran, which resulted in a $20.0 million milestone payment to the Company. During the three ~~and six~~ months ended ~~March~~December 31, 2021 and 2020, the Company recognized $0 and $0 of revenue associated with its agreement with Amgen, respectively.As of ~~March~~December 31, 2021, there were $0 in contract assets recorded as accounts receivable and $0 of contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets.

On October 3, 2018, the Company entered into ~~the Janssen~~a License Agreement (the “Janssen License Agreement”) and ~~the Janssen~~a Research Collaboration and Option Agreement (the “Janssen Collaboration Agreement”) with Janssen, part of the Janssen Pharmaceutical Companies of Johnson & Johnson. The Company also entered into a stock purchase agreement with JJDC (“JJDC Stock Purchase Agreement”). Under the Janssen License Agreement, Janssen has received a worldwide, exclusive license to the Company’s JNJ-3989 (ARO-HBV) program, the Company’s third-generation subcutaneously administered RNAi therapeutic candidate being developed as a potential therapy for patients with chronic hepatitis B virus infection. Beyond the Company’s Phase 1/2 study of JNJ-3989 (ARO-HBV), which the Company was responsible for completing, Janssen is ~~also~~ wholly responsible for clinical development and commercialization of JNJ-3989. Under the Janssen Collaboration Agreement, Janssen will be able to select three new targets against which Arrowhead will develop clinical candidates. These candidates are subject to certain restrictions and do not include candidates that already were in the Company’s pipeline. The Company will perform discovery, optimization and preclinical research and development, entirely funded by Janssen, which on its own or in combination with Janssen development work, is sufficient to allow the filing of a U.S. Investigational New Drug Application or equivalent, at which time Janssen will have the option to take an exclusive license. If the option is exercised, Janssen will be wholly responsible for clinical development and commercialization of each optioned candidate. Under the terms of the agreements taken together, the Company has received $175.0 million as an upfront payment, $75.0 million in the form of an equity investment by JJDC in Arrowhead Common Stock under the JJDC Stock Purchase Agreement, and ~~two $25.0~~milestone and option payments totaling $70.0 million, ~~milestone payments,~~ and the Company may receive up to $1.6 billion in development and sales milestones payments for the Janssen License Agreement, and up to $1.9 billion in development and sales milestone payments for the 3 additional targets covered under the Janssen Collaboration Agreement. The Company is further eligible to receive tiered royalties on product sales up to mid-teens under the Janssen License Agreement and up to low teens under the Janssen Collaboration ~~Agreement on product sales.~~Agreement.

The Company has evaluated these agreements in accordance with FASB ~~Topic~~Topics 808 – Collaboration Arrangements and 606 - Revenue for Contracts from ~~Customers, which became effective for the Company on October 1, 2018.~~Customers. At the inception of these agreements, the Company identified 1 distinct performance obligation. Regarding the Janssen License Agreement, the Company determined that the key deliverables included the license and certain R&D services including the Company’s responsibility to complete the Phase 1/2 study of JNJ-3989 (ARO-HBV) and the Company’s responsibility to ensure certain manufacturing of JNJ-3989 (ARO-HBV) drug product is completed and delivered to Janssen (the “Janssen R&D Services”). Due to the specialized and unique nature of these Janssen R&D Services and their direct relationship with the license, the Company determined that these deliverables represent one distinct bundle and, thus, one performance obligation. The Company also determined that Janssen’s option to require the Company to develop up to three new targets is not a material right and, thus, not a performance obligation at the onset of the agreement. The consideration for this option is accounted for separately.

The Company determined the transaction price totaled approximately $252.7 million, which includes the upfront payment, the premium paid by JJDC for its equity investment in the Company, ~~the~~ two $25.0 million milestone payments ~~earned~~related to JNJ-3989 (ARO-HBV), and estimated payments for reimbursable Janssen R&D Services to be performed. The Company has allocated the total $252.7 million initial transaction price to its one distinct performance obligation for the JNJ-3989 (ARO-HBV) license and the associated Janssen R&D Services. ~~This revenue~~The Company has recognized this transaction price in its entirety as of September 30, 2021, as its performance obligations were substantially completed. Future milestones and royalties achieved will be recognized ~~using a proportional performance method (based on actual costs incurred versus total estimated costs incurred) beginning~~ in ~~October 2018 and ending as the Company’s efforts in overseeing the Phase 1/2 clinical trial are completed.~~their entirety when earned. During the three months ended ~~March~~December 31, 2021 and 2020, the Company recognized approximately ~~$7.5 million~~$0 and ~~$22.2 million of revenue associated with this performance obligation, respectively. During the six months ended March 31, 2021 and 2020, the Company recognized approximately $20.2 million and $50.9~~$12.7 million of revenue associated with this performance obligation, respectively. As of ~~March~~December 31, 2021, there were ~~$0.6 million~~$0 in contract assets recorded as accounts receivable, and $0 of contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets.

The Company has begun to conduct its discovery, optimization and preclinical research and development of ~~ARO-JNJ1,~~JNJ-75220795 (ARO-JNJ1), ARO-JNJ2 and ARO-JNJ3 under the Janssen Collaboration Agreement. All costs and labor hours spent by the Company will be entirely funded by Janssen. During the three months ended ~~March~~December 31, 2021 and 2020, the Company recognized ~~$0.1 million~~$0 and ~~$1.4~~$0.3 million of revenue associated with these efforts, respectively. ~~During the six months ended March 31, 2021 and 2020, the Company recognized $0.3 million and $2.1 million of revenue associated with these efforts, respectively.~~ As of ~~March~~December 31, 2021, there were ~~$0.3 million~~$0 of contract assets recorded as accounts receivable and $0 of contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets.

On October 7, 2020, the Company entered into ~~the Takeda~~an Exclusive License ~~Agreement~~and Co-funding agreement (the “Takeda License Agreement”) with Takeda. Under the Takeda License Agreement, Takeda and the Company will co-develop the Company’s ARO-AAT program, the Company’s second-generation subcutaneously administered RNAi therapeutic candidate being developed as a treatment for liver disease associated with alpha-1 antitrypsin deficiency. Within the United States, ARO-AAT, if approved, will be co-commercialized under a 50/50 profit sharing structure. Outside the United States, Takeda will lead the global commercialization strategy and will receive an exclusive license to commercialize ARO-AAT, ~~with~~while the Company will be eligible to receive tiered royalties of 20% to 25% on net sales. In January 2021, the Company received $300.0 million as an upfront payment and is eligible to receive potential development, regulatory and commercial milestones of up to $740.0 million.

The Company has evaluated the Takeda License Agreement in accordance with FASB ~~Topic~~Topics 808 – Collaborative Arrangements and 606 - Revenue for Contracts from ~~Customers, which became effective for the Company on October 1, 2018.~~Customers. At the inception of the Takeda License Agreement, the Company identified 1 distinct performance obligation. The Company determined that the key deliverables included the license and certain R&D services including the Company’s responsibilities to complete the initial portion of the SEQUOIA study, to complete the ongoing Phase 2 AROAAT2002 study and to ensure certain manufacturing of ARO-AAT drug product is completed and delivered to Takeda (the “Takeda R&D Services”). Due to the specialized and unique nature of these Takeda R&D Services and their direct relationship with the license, the Company determined that these deliverables represent 1 distinct bundle and, thus, one performance obligation. Beyond the Takeda R&D Services, which are the responsibility of the Company, Takeda will be responsible for managing future clinical development and ~~commercialization.~~commercialization outside the United States. Within the United States, the Company will also participate in co-development and co-commercialization efforts and will co-fund these efforts with Takeda as part of the 50/50 profit sharing structure within the United States. The Company ~~will co-fund certain~~considers the collaborative activities, including the co-development and co-commercialization, to be a separate unit of ~~the development~~account within Topic 808, and ~~commercialization costs that Takeda manages, and~~as such, these co-funding amounts will be ~~offset against amounts owed to Arrowhead, either from milestones~~recorded as Research and Development Expenses or ~~royalties earned, or profits earned under the 50/50 profit sharing structure for U.S. commercialization.~~General and Administrative Expenses, as appropriate.

The Company determined the initial transaction price totaled ~~approximately~~ $300.0 million, which includes the upfront payment. The Company ~~will exclude~~has excluded any future ~~estimated~~ milestones ~~royalties,~~ or ~~profit-sharing payments~~royalties from this transaction price to date. The Company ~~will allocate~~has allocated the total $300.0 million initial transaction price to its one distinct performance obligation for the ARO-AAT license and the associated Takeda R&D Services. Revenue will be recognized using a proportional performance method (based on actual ~~costs incurred~~patient visits completed versus total estimated ~~costs incurred~~visits completed for the ~~Takeda R&D Services)~~ongoing SEQUOIA and AROAAT2002 clinical studies). Revenue for the three months ended ~~March~~December 31, 2021 and 2020 ~~were $25.4~~was $20.8 million and ~~$0, respectively. Revenue for the six months ended March 31, 2021 and 2020 were $33.6~~$8.2 million, ~~and $0,~~ respectively. As of ~~March~~December 31, 2021, there were $0 in contract assets recorded as accounts receivable, ~~$144.9~~$82.0 million in contract liabilities recorded as deferred revenue and ~~$121.5~~$106.5 million in contract liabilities recorded as deferred revenue, net of the current ~~portion.~~portion, and $2.9 million in contract liabilities recorded as accrued expenses. The $2.9 million in accrued expenses was primarily driven by co-development and co-commercialization activities.

On June 18, 2021, the Company entered into the Horizon License Agreement with Horizon. Under the Horizon License Agreement, Horizon received a worldwide exclusive license for ARO-XDH, a previously undisclosed discovery-stage investigational RNAi therapeutic being developed by the Company as a potential treatment for people with uncontrolled gout. The Company will conduct all activities through the preclinical stages of development of ARO-XDH, and Horizon will be wholly responsible for clinical development and commercialization of ARO-XDH. In July 2021, the Company received $40 million as an upfront payment and is eligible to receive up to $660 million in potential development, regulatory and sales milestones. The Company is also eligible to receive royalties in the low- to mid-teens range on net product sales.

The Company has evaluated the Horizon License Agreement in accordance with FASB Topics 808 – Collaborative Arrangements and 606 - Revenue for Contracts from Customers. At the inception of the Horizon License Agreement, the Company identified one distinct performance obligation. The Company determined that the key deliverables included the license and certain R&D services, including the Company’s responsibilities to conduct all activities through the preclinical stages of development of ARO-XDH (the “Horizon R&D Services”). Due to the specialized and unique nature of these Horizon R&D Services and their direct relationship with the license, the Company determined that these deliverables represented 1 distinct bundle and, thus, 1 performance obligation. Beyond the Horizon R&D Services, which are the responsibility of the Company, Horizon will be responsible for managing future clinical development and commercialization of ARO-XDH.

The Company determined the initial transaction price totaled $40.0 million, including the upfront payment. The Company has excluded any future estimated milestones or royalties, from this transaction price to date. The Company will allocate the total $40.0 million initial transaction price to its 1 distinct performance obligation for the ARO-XDH license and the associated Horizon R&D Services. Revenue will be recognized on a straight-line basis over the estimated timeframe for completing the Horizon R&D Services. The Company determined that the straight-line basis was appropriate as its efforts will be expended evenly over the course of completing its performance obligation. Revenue for the three months ended December 31, 2021 and 2020 was $6.7 million and $0, respectively. As of December 31, 2021, there were $0.1 million in contract assets recorded as accounts receivable, $26.7 million in contract liabilities recorded as deferred revenue.

On November 22, 2021, the Company entered into an Exclusive License Agreement (the “GSK License Agreement”) with GSK. Under the GSK License Agreement, GSK has received an exclusive license for ARO-HSD, the Company’s investigational RNAi therapeutic being developed as a treatment for patients with alcohol-related and nonalcohol related liver diseases, such as nonalcoholic steatohepatitis (NASH). The exclusive license is worldwide with the exception of greater China, for which the Company will retain rights to develop and commercialize. Beyond the Company’s Phase 1/2 study of (ARO-HSD), which the Company is responsible for completing, GSK is wholly responsible for clinical development and commercialization of ARO-HSD in its territory. Under the terms of the agreement, the Company has received an upfront payment of $120 million and is eligible for additional payments of $30 million at the start of Phase 2 and $100 million upon achieving a successful Phase 2 trial readout and the first patient dosed in a Phase 3 trial. Furthermore, should the Phase 3 trial read out positively, and the potential new medicine receives regulatory approval in major markets, the deal provides for commercial milestone payments to the Company of up to $190 million at first commercial sale, and up to $590 million in sales-related milestone payments. The Company is further eligible to receive tiered royalties on net product sales in a range of mid-teens to twenty percent.

The Company has evaluated the GSK License Agreement in accordance with FASB Topics 808 – Collaborative Arrangements and 606 - Revenue for Contracts from Customers. At the inception of the GSK License Agreement, the Company identified 1 distinct performance obligation. The Company determined that the key deliverables included the license and certain R&D services, including the Company’s responsibility to complete the Phase 1/2 study, (the “GSK R&D Services”). Due to the specialized and unique nature of these GSK R&D Services and their direct relationship with the license, the Company determined that these deliverables represented 1 distinct bundle and, thus, one performance obligation. Beyond the GSK R&D Services, which are the responsibility of the Company, GSK will be responsible for managing future clinical development and commercialization in its territory.

The Company determined the initial transaction price totaled $120.0 million, including the upfront payment. The Company has excluded any future estimated milestones or royalties from this transaction price to date. The Company has allocated the total $120.0 million initial transaction price to its one distinct performance obligation for the ARO-HSD license and the associated GSK R&D Services. Revenue will be recognized using a proportional performance method. As of December 31, 2021, 0 revenue or contract assets or liabilities were recognized as the GSK License Agreement had not yet completed customary closing conditions, including clearance by the relevant competition authorities. This clearance was achieved in January 2022 and the upfront payment of $120.0 million was also received by the Company in January 2022.

The following table summarizes the Company’s major classes of property and equipment:

	March 31, 2021			September 30, 2020			December 31, 2021			September 30, 2021
	(In thousands)						(In thousands)
Computers, office equipment and furniture	$	1,022		$	662
Computers, software, office equipment and furniture							$	2,182		$	2,170
Research equipment		23,894			20,654			28,010			27,500
Software		599			631
Leasehold improvements		33,107			25,238			41,977			41,524
Construction in Progress								2,152			345
Land								2,996			-
Total gross fixed assets		58,622			47,185			77,317			71,539
Less: Accumulated depreciation and amortization		(19,222	)		(16,304	)		(25,014	)		(22,864	)
Property and equipment, net	$	39,400		$	30,881		$	52,303		$	48,675

Depreciation and amortization expense for property and equipment for the three months ended ~~March~~December 31, 2021 and 2020 was ~~$1.5~~$2.1 million and ~~$0.9~~$1.4 million, respectively. ~~Depreciation~~Construction in Progress and ~~amortization expense for property and equipment for~~Land both relate to the ~~six months ended March 31, 2021 and 2020 was $2.9 million and $1.8 million, respectively.~~Company’s Verona, Wisconsin research facility.

Investments at ~~March~~December 31, 2021 primarily consisted of corporate bonds that have maturities of less than 36 months, a certificate of deposit and marketable equity securities. The Company’s corporate bonds consist of both short-term and long-term bonds and are classified as “held-to-maturity” on the Company’s Consolidated Balance Sheets. The Company’s certificate of deposit matures in less than 12 months and is classified as “held-to-maturity” on the Company’s Consolidated Balance Sheet. The Company’s marketable equity securities consist of mutual funds that primarily invest in U.S. government bonds, U.S. government agency bonds, corporate bonds and other asset-backed debt securities. Dividends from these funds are automatically ~~reinvested.~~re-invested. The Company may also invest excess cash balances in ~~certificates of deposits,~~ money market accounts, government-sponsored enterprise securities, ~~corporate bonds~~ and/or commercial paper. The Company accounts for its held to maturity investments in accordance with FASB ASC 320, Investments – Debt and Equity Securities and its marketable equity securities in accordance with ASC 321, Investments – Equity Securities.

The following tables summarize the Company’s short-term and long-term investments and marketable securities as of ~~March~~December 31, 2021 and September 30, ~~2020~~2021 by measurement ~~category.~~category:

Held to Maturity	As of March 31, 2021									As of December 31, 2021
	(In thousands)									(In thousands)
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Commercial notes (due within one year)	$	79,148	$	887	$	-		$	80,035	$	62,537	$	687	$	-		$	63,224
Commercial notes (due within one through three years)	$	97,490	$	2,655	$	(66	)	$	100,079	$	217,572	$	381	$	(1,374	)	$	216,579
Certificate of deposit (due within one year)										$	50,000	$	-	$	-		$	50,000
Total	$	176,638	$	3,542	$	(66	)	$	180,114	$	330,109	$	1,068	$	(1,374	)	$	329,803

	As of September 30, 2020									As of September 30, 2021
	(In thousands)									(In thousands)
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value		Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Commercial notes (due within one year)	$	86,890	$	1,590	$	-		$	88,480	$	56,627	$	803	$	-		$	57,430
Commercial notes (due within one through three years)	$	137,487	$	4,573	$	(79	)	$	141,981	$	195,595	$	1,151	$	(103	)	$	196,643
Certificate of deposit (due within two years)										$	50,000	$	-	$	-		$	50,000
Total	$	224,377	$	6,163	$	(79	)	$	230,461	$	302,222	$	1,954	$	(103	)	$	304,073

Fair Value	As of March 31, 2021											As of December 31, 2021
	(In thousands)											(In thousands)
	Cost		Realized Gains/(Losses)		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value		Cost		Realized Gains/(Losses)		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Marketable securities	$	125,000	$	1,079	$	205	$	(491	)	$	125,793	$	125,000	$	3,134	$	-	$	(2,124	)	$	126,010
Total	$	125,000	$	1,079	$	205	$	(491	)	$	125,793	$	125,000	$	3,134	$	-	$	(2,124	)	$	126,010

	As of September 30, 2020											As of September 30, 2021
	(In thousands)											(In thousands)
	Cost		Realized Gains/(Losses)		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value		Cost		Realized Gains/(Losses)		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Marketable securities	$	85,000	$	95	$	-	$	(75	)	$	85,020	$	125,000	$	2,481	$	135	$	(888	)	$	126,728
Total	$	85,000	$	95	$	-	$	(75	)	$	85,020	$	125,000	$	2,481	$	135	$	(888	)	$	126,728

Realized gains for marketable securities recorded at fair value consist of dividends received and re-invested into the associated fund.

Intangible assets subject to amortization include patents and a license agreement capitalized as part of the Novartis RNAi asset acquisition in March 2015. The license agreement associated with the Novartis RNAi asset acquisition is being amortized over the estimated life remaining at the time of acquisition, which was 21 years, and the accumulated amortization of the asset is ~~$0.9~~$1.0 million. The patents associated with the Novartis RNAi asset acquisition are being amortized over the estimated life remaining at the time of acquisition, which was 14 years, and the accumulated amortization of the assets is ~~$9.4~~$10.6 million. Amortization expense for the three months ended ~~March~~December 31, 2021 and 2020 was $0.4 million and $0.4 million, respectively. Amortization expense ~~for the six months ended March 31, 2021 and 2020 was $0.9 million and $0.9 million, respectively. Amortization expense~~ is expected to be ~~$0.9~~$1.3 million for the remainder of ~~2021, $1.7 million in~~ fiscal2022, $1.7 million in 2023, $1.7 million in 2024, $1.7 million in 2025, $1.7 million in 2026 and ~~$6.8~~$5.2 million thereafter.

The following table provides details on the Company’s intangible asset balances:

	Intangible assets subject to amortization			Intangible Assets Subject to Amortization
	(in thousands)			(in thousands)
Balance at September 30, 2020	$	15,363
Balance at September 30, 2021				$	13,663
Impairment		-			-
Amortization		(850	)		(425	)
Balance at March 31, 2021	$	14,513
Balance at December 31, 2021				$	13,238

At ~~March~~December 31, 2021, the Company had a total of 150,000,000 shares of capital stock authorized for issuance, consisting of 145,000,000 shares of Common Stock, par value $0.001 per share, and 5,000,000 shares of Preferred Stock, par value $0.001 per share.

At ~~March~~December 31, 2021, ~~104,019,546~~104,798,186 shares of Common Stock were outstanding. At ~~March~~December 31, 2021, ~~16,819,225~~14,834,548 shares of Common Stock were reserved for issuance upon exercise of options and vesting of restricted stock units granted or available for grant under Arrowhead’s 2004 Equity Incentive Plan, 2013 Incentive Plan, and 2021 Incentive Plan, as well as for inducement grants made to new ~~employees.~~employees under Rule 5635(c)(4) of the Nasdaq Listing Rules.

10In August 2020, the Company entered into an Open Market Sale Agreement (the “ATM Agreement”), pursuant to which the Company may, from time to time, sell up to $250,000,000 in shares of the Company’s Common Stock through Jefferies LLC, acting as the sales agent and/or principal, in an at-the-market offering. The Company is not required to sell shares under the ATM Agreement. The Company will pay Jefferies LLC a commission of up to 3.0% of the aggregate gross proceeds received from all sales of the common stock under the ATM Agreement. Unless otherwise terminated, the ATM Agreement continues until the earlier of selling all shares available under the ATM Agreement or December 2, 2022. At December 31, 2021, 0 shares have been sold under the ATM Agreement.

From time to time, the Company may be subject to various claims and legal proceedings in the ordinary course of business. If the potential loss from any claim, asserted or unasserted, or legal proceeding is considered probable and the amount is reasonably estimable, the Company will accrue a liability for the estimated loss. There were 0 contingent liabilities recorded as of ~~the six months ended March~~December 31, 2021.

~~In the normal course of business,~~On December 20, 2021, the Company ~~enters into various~~completed a purchase ~~commitments for~~of 13 acres of land in the ~~manufacture of drug components, for toxicology studies and for clinical studies. As of March 31, 2021, these future commitments were estimated at approximately $136.0 million, of~~Verona Technology Park in Verona, WI, which ~~approximately $78.0 million~~ is ~~expected~~planned to be ~~incurred during~~ the ~~remainder~~site of ~~fiscal year 2021.~~an approximately 140,000 square foot drug manufacturing facility and an approximately 115,000 square foot laboratory and office facility to support process development and analytical activities. Arrowhead intends to invest between $200 million and $250 million into the buildout of the facilities. As part of this acquisition, the Company also entered into a development agreement with the City of Verona to construct certain infrastructure improvements within the TIF district, and will be reimbursed by the City of Verona by future tax increment revenue generated from the developed property. The total amount of funding that City of Verona will pay as reimbursements under the TIF program for these improvements is not guaranteed and will depend on future tax revenues generated from the developed property.

The Company has licensed from third parties the rights to use certain technologies for its research and development activities, as well as in any products the Company may develop using these licensed technologies. These agreements and other similar agreements often require milestone and royalty payments. Milestone payments, for example, may be required as the research and development process progresses through various stages of development, such as when clinical candidates enter or progress through clinical trials, upon a new drug application and upon certain sales level milestones. These milestone payments could amount to the mid to upper double-digit millions of dollars. During the three ~~and six~~ months ended ~~March~~December 31, 2021 and 2020, the Company did 0t reach any milestones. ~~During the three and six months ended March 31, 2020, the Company accrued a $0.9 million milestone payment related to the progression of the ARO-ENaC program. In~~Under certain agreements, the Company may be required to make mid to high single-digit percentage royalty payments based on a percentage of ~~the~~ sales of the relevant products.

In April 2019, the Company entered into a lease for its corporate headquarters in Pasadena, California. The 91 month office building lease between the Company and 177 Colorado Owner, LLC is for approximately 24,000 square feet of office space located at 177 E. Colorado Blvd, Pasadena, California. The increased capacity of this new office space compared to the Company’s prior corporate headquarters will accommodate increased personnel as the Company’s pipeline of drug candidates expands and moves closer to market. Lease payments began on September 30, 2019 and are estimated to total approximately $8.7 million over the term. The lease expires on April 30, 2027. The Company has paid approximately $3.5 million for leasehold improvements, net of tenant improvement allowances. The lease contains an option to renew for 1 ~~additional~~ term of five years. The exercise of this option was not determined to be reasonably certain and thus was not included in lease liabilities on the Company’s Consolidated Balance Sheet at ~~March~~December 31, 2021. On October 23, 2020, the Company entered into a lease expansion to add an additional approximately 24,000 square feet of office space at the same location for its corporate headquarters. ~~The lease commencement date is expected to be~~Lease payments for the expansion began in ~~June~~July 2021 ~~after certain leasehold improvements are completed,~~ and the lease for the expansion expires in April 2027. The lease payments for the expansion are expected to total $6.9 million. The Company ~~anticipates paying~~has paid approximately ~~$4.2~~$4.0 million of leasehold improvements, net of tenant improvement ~~allowances.~~allowances, for the lease expansion. The increased capacity of this additional office space compared to the Company’s current corporate headquarters ~~will~~is intended to accommodate increased personnel as the Company’s pipeline of drug candidates ~~expands~~continues to expand and ~~moves~~move closer to market.

In January 2016, the Company entered into a lease for its research facility in Madison, Wisconsin. The lease was for approximately 60,000 square feet of office and laboratory space and had an expiration date of September 30, 2026. The lease was amended in January 2019 and May 2020 to expand the rentable square feet by an additional 40,000 ~~total~~ square feet and to extend the lease expiration date to September 30, 2031. Lease payments are estimated to total approximately $26.2 million for the term. The Company ~~anticipates paying~~incurred approximately $11.0 million of leasehold improvements for the additional 40,000 square feet, net of tenant improvement allowances. The lease contains 2 options to renew for two ~~additional~~ terms of five years. The exercise of these options were not determined to be reasonably certain and thus was not included in lease liabilities on the Company’s Consolidated Balance Sheet at ~~March~~December 31, 2021. In November 2020 and December 2020, the Company entered into amendments to expand the rentable square space by an additional 10,743 square feet and these amendments added a total of approximately $1.2 million of lease payments for the remainder of the term.

In March 2020, the Company entered into a sublease agreement ~~(the “Sublease”) with Halozyme, Inc.~~ for additional research and development facility space in San Diego, California. The Sublease provides additional space needed to accommodate the recent growth of the Company’s personnel and discovery efforts. The Sublease is for approximately 21,000 rentable square feet. The term of the Sublease commenced on April 1, 2020 and will end on January 14, 2023. Sublease payments are estimated to total approximately $2.0 million over the term.

On November 19, 2021, the Company entered into a new lease for a San Diego, California research facility. The 15-year lease is for approximately 144,000 square feet of office and research and development laboratory space to be constructed in San Diego, California. This lease will replace the Company’s current research facility sublease for property located in San Diego, California. The increased capacity of this new facility compared to the Company’s current research facility in San Diego will accommodate increased personnel for the Company’s expanding pipeline of current and future drug candidates. The estimated rent commencement date for the lease is in May 2023, after construction and leasehold improvements have been completed. The lease payments, which begin on the rent commencement date, will be approximately $119.0 million over the initial 15-year term. The Company also estimates payments for operating expenses to be approximately $3.0 million for the first year of the lease, and these payments will continue throughout the initial 15-year term. The Company expects to pay approximately $31.0 million for leasehold improvements, net of tenant improvement allowances. Pursuant to the lease, within twelve months of the expiration of the initial 15-year term, the Company has the option to extend the lease for up to 1 additional ten-year term, with certain annual increases in base rent. No lease liabilities have been recorded as of December 31, 2021 as the lease commencement date has not yet occurred.

Operating lease cost during the three months ended ~~March~~December 31, 2021 and 2020 was ~~$1.1 million and $0.5 million, respectively. Operating lease cost during the six months ended March 31, 2021 and 2020 was $2.0~~$1.3 million and $0.9 million, respectively. Variable lease costs for the three months ended ~~March~~December 31, 2021 and 2020 was $0.2 million and $0.2 million, respectively. ~~Variable lease costs for the six months ended March 31, 2021 and 2020 was $0.5 million and $0.3 million, respectively.~~ There was 0 short-term lease cost during the three ~~and six~~ months ended ~~March~~December 31, 2021 and 2020.

The following table presents maturities of operating lease liabilities on an undiscounted basis as of ~~March~~December 31, 2021:

	(in thousands)			(in thousands)
2021 (remainder of fiscal year)	$	1,740
2022		4,522		$	3,685
2023		4,624			4,786
2024		4,523			4,621
2025		4,649			4,749
2026 and thereafter		17,421
2026					5,050
2027 and thereafter					13,200
Total	$	37,479		$	36,091
Less imputed interest	$	(13,679	)	$	(10,776	)
Total operating lease liabilities (includes current portion)	$	23,800		$	25,315

Cash paid for the amounts included in the measurement of the operating lease liabilities on the Company’s Consolidated Balance Sheet and included in Other changes in operating assets and liabilities within cash flows from operating activities on the Company’s Consolidated ~~Statement~~Statements of Cash ~~Flow~~Flows for the ~~six~~three months ended ~~March~~December 31, 2021 and 2020 was ~~$1.4~~$1.0 million and ~~$0.6~~$0.7 million, respectively. The weighted-average remaining lease term and weighted-average discount rate for all leases as of ~~March~~December 31, 2021 was ~~8.5~~7.8 years and 8.5%, respectively.

Arrowhead has three plans that provide for equity-based compensation. Under the 2004 Equity Incentive Plan and the 2013 Incentive Plan, as of ~~March~~December 31, 2021, ~~468,993~~376,301 and ~~6,593,291~~4,904,814 shares, respectively, of Arrowhead’s Common Stock are reserved for the grant of stock options, stock appreciation rights, and restricted stock ~~awards and performance unit/share~~unit awards to employees, consultants and others. No further grants may be made under the 2004 Equity Incentive Plan. As of ~~March~~December 31, 2021, there were options granted and outstanding to purchase ~~468,993~~376,301 and ~~2,229,852~~1,948,814 shares of Common Stock under the 2004 Equity Incentive Plan and the 2013 Incentive Plan, respectively, and there were ~~3,177,950~~2,956,000 restricted stock units granted and outstanding under the 2013 Incentive Plan. Also, as of ~~March~~December 31, 2021, there were ~~1,080,741~~889,890 shares reserved for options and ~~676,200~~651,000 shares reserved for restricted stock units issued as inducement grants to new employees outside of equity compensation plans. ~~On March 18, 2021,~~Under the ~~Company’s stockholders approved the Arrowhead Pharmaceuticals, Inc.~~ 2021 Incentive Plan, (“as of December 31, 2021, ~~Incentive Plan”), which authorizes 8,000,000~~3,000 shares ~~(subject to certain adjustments) to be awarded for grants~~ of ~~stock options, stock appreciation rights,~~Common Stock and 76,400 restricted ~~and unrestricted stock and~~ stock units ~~performance awards, cash awards~~were granted and ~~other awards convertible into or otherwise based on shares of Arrowhead’s Common Stock. The maximum number of shares authorized~~outstanding under the 2021 Incentive Plan will be (i) reduced by any shares subject to awards made under the 2013 Incentive Plan after January 1, 2021, and (ii) increased by any shares subject to outstanding awards under the 2013 Incentive Plan as of January 1, 2021 that, after January 1, 2021, are canceled, expired, forfeited or otherwise not issued under such awards (other than as a result of being tendered or withheld to pay the exercise price or withholding taxes in connection with any such awards) or settled in cash.Plan. As of ~~March~~December 31, 2021, ~~there had been no adjustments to~~ the ~~8,000,000~~total number of authorized shares under the 2021 Incentive Plan ~~and 0~~was 8,012,543 shares, ~~of Arrowhead’s Common Stock had been granted~~which includes 91,943 shares that were forfeited under the ~~2021~~2013 Incentive Plan.

	Number of Options Outstanding			Weighted- Average Exercise Price Per Share		Weighted- Average Remaining Contractual Term	Aggregate Intrinsic Value		Number of Options Outstanding			Weighted- Average Exercise Price Per Share		Weighted- Average Remaining Contractual Term	Aggregate Intrinsic Value
Balance at September 30, 2020		4,539,403		$	16.67
Balance at September 30, 2021										3,456,239		$	19.60
Granted		168,000		65.41						-			-
Cancelled		(108,149	)	28.85						(30,420	)	35.57
Exercised		(819,668	)	9.44						(207,814	)	10.32
Balance at March 31, 2021		3,779,586		$	20.06	6.1 years	$	175,292,764
Exercisable at March 31, 2021		2,426,786		$	10.64	4.8 years	$	135,141,412
Balance at December 31, 2021										3,218,005		$	20.05	5.4 years	$	149,311,699
Exercisable at December 31, 2021										2,460,188		$	13.69	4.6 years	$	129,520,403

Stock-based compensation expense related to stock options for the three months ended ~~March~~December 31, 2021 and 2020 was ~~$3.3~~$3.0 million and ~~$2.5 million, respectively. Stock-based compensation expense related to stock options for the six months ended March 31, 2021 and 2020 was $6.4 million and $4.1~~$3.1 million, respectively. For non-qualified stock options, the expense creates a timing difference, resulting in a deferred tax asset, which is fully reserved by a valuation allowance.

The grant date fair value of the options granted by the Company for the three months ended ~~March~~December 31, 2021 and 2020 was ~~$1.4 million~~$0 and ~~$18.0 million, respectively. The grant date fair value of the options granted by the Company for the six months ended March 31, 2021 and 2020 was $8.1 million and $26.6~~$6.8 million, respectively.

The intrinsic value of the options exercised during the three months ended ~~March~~December 31, 2021 and 2020 was ~~$20.9~~$12.5 million and ~~$8.6 million, respectively. The intrinsic value of the options exercised during the six months ended March 31, 2021 and 2020 was $52.8 million and $30.2~~$32.0 million, respectively.

As of ~~March~~December 31, 2021, the pre-tax compensation expense for all outstanding unvested stock options in the amount of ~~$35.7~~$22.4 million will be recognized in the Company’s results of operations over a weighted average period of ~~2.9~~2.2 years.

The fair value of each stock option award is estimated on the date of grant using the Black-Scholes option pricing model. The Black-Scholes option valuation model was developed for use in estimating the fair value of traded options, which do not have vesting restrictions and are fully transferable. The determination of the fair value of each stock option is affected by the Company’s stock price on the date of grant, as well as assumptions regarding a number of highly complex and subjective variables. Because the Company’s employee stock options have characteristics significantly different from those of traded options, and because changes in the subjective input assumptions can materially affect the fair value estimate, in management’s opinion, the existing models do not necessarily provide a reliable single measure of the fair value of its employee stock options.

	Six Months Ended March 31,				Three Months Ended December 31,
	2021		2020		2021	2020
Dividend yield		-		-	N/A		-
Risk-free interest rate	0.4 – 0.6%		0.5-1.8%		N/A	0.4 – 0.6%
Volatility	86.6 – 90.4%		90.5 – 91.8%		N/A	90.0 – 90.4%
Expected life (in years)		6.25		6.25	N/A		6.25
Weighted average grant date fair value per share of options granted	$	48.62	$	40.70	N/A	$	47.34

Volatility is estimated based on volatility average of the Company’s Common Stock price.

Restricted stock units (“RSUs”), including time-based, market condition-based, and ~~performance-based~~performance condition-based awards, ~~were~~have been granted under the Company’s 2013 Incentive Plan, 2021 Incentive Plan, and as inducements grants granted outside of the Company’s equity-based compensation ~~plans. During~~plans under Rule 5635(c)(4) of the three months ended March 31, 2021, the Company issued 1,324,750 RSUs under the 2013 Incentive Plan and 0 RSUs as inducement awards. During the six months ended March 31, 2021, the Company issued 1,326,950 RSUs under the 2013 Incentive Plan and 116,000 RSUs as inducement awards.Nasdaq Listing Rules. At vesting, each outstanding RSU will be exchanged for one share of the Company’s Common Stock. RSU awards generally vest subject to the satisfaction of service requirements or the satisfaction of both service requirements and achievement of certain performance targets.

	Number of RSUs			Weighted- Average Grant Date Fair Value		Number of RSUs			Weighted- Average Grant Date Fair Value
Unvested at September 30, 2020		3,524,025		$	44.11
Unvested at September 30, 2021							3,731,850		$	60.82
Granted		1,442,950			75.54		122,500			62.60
Vested		(823,575	)		30.11		(263,700	)		61.11
Forfeited		(289,250	)		39.14		(7,250	)		83.54
Unvested at March 31, 2021		3,854,150		$	59.24
Unvested at December 31, 2021							3,583,400		$	60.82

During the three months ended ~~March~~December 31, 2021 and 2020, the Company recorded ~~$12.1~~$21.5 million and ~~$10.4 million of expense related to RSUs, respectively. During the six months ended March 31, 2021 and 2020, the Company recorded $17.1 million and $13.3~~$5.0 million of expense related to RSUs, respectively. Such expense is included in stock-based compensation expense in the Company’s Consolidated ~~Statement~~Statements of Operations and Comprehensive Income (Loss). For RSUs, the expense creates a timing difference, resulting in a deferred tax asset, which is fully reserved by a valuation allowance.

For RSUs, the grant date fair value of the award is based on the Company’s closing stock price at the grant date, with consideration given to the probability of achieving performance conditions for performance-based awards. The grant date fair value of the RSUs granted by the Company for the three months ended ~~March~~December 31, 2021 and 2020 was ~~$101.6~~$7.7 million and ~~$122.0 million, respectively. The grant date fair value of the RSUs granted by the Company for the six months ended March 31, 2021 and 2020 was $109.0 million and $136.0~~$7.4 million, respectively.

As of ~~March~~December 31, 2021, the pre-tax compensation expense for all unvested RSUs in the amount of ~~$131.4~~$139.7 million will be recognized in the Company’s results of operations over a weighted average period of ~~3.1~~2.6 years. ~~Unvested RSUs that we have deemed not probable of vesting as of March~~

During the three months ended December 31, 2021, ~~have the potential of generating~~certain performance condition-based awards were modified to either add an additional ~~$76.4 million~~market condition component, or to replace performance conditions with market conditions entirely. The Company assessed the modification date fair value based on a monte carlo simulation model. The fair value of ~~pre-tax compensation expense if we deem them probable of vesting in a future reporting period.~~ market condition-based awards is expensed ratably over the service period and is not adjusted for actual achievement.

The Company measures its financial assets and liabilities at fair value. Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability (i.e., exit price) in an orderly transaction between market participants at the measurement date. Additionally, the Company is required to provide disclosure and categorize assets and liabilities measured at fair value into one of three different levels depending on the assumptions (i.e., inputs) used in the valuation. Level 1 provides the most reliable measure of fair value while Level 3 generally requires significant management judgment. Financial assets and liabilities are classified in their entirety based on the lowest level of input significant to the fair value measurement. The fair value hierarchy is defined as follows:

Level 1—Valuations are based on unadjusted quoted prices in active markets for identical assets or liabilities.

Level 2—Valuations are based on quoted prices for similar assets or liabilities in active markets, or quoted prices in markets that are not active for which significant inputs are observable, either directly or indirectly.

Level 3—Valuations are based on prices or valuation techniques that require inputs that are both unobservable and significant to the overall fair value measurement. Inputs reflect management’s best estimate of what market participants would use in valuing the asset or liability at the measurement date.

The following table summarizes fair value measurements at ~~March~~December 31, 2021 and September 30, ~~2020~~2021 for assets and liabilities measured at fair value on a recurring ~~basis.~~basis:

	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
	(in thousands)								(in thousands)
Cash and cash equivalents	$	372,377	$	-	$	-	$	372,377	$	91,587	$	-	$	-	$	91,587
Marketable securities	$	125,793	$	-	$	-	$	125,793	$	126,010	$	-	$	-	$	126,010
Short-term investments (held to maturity)	$	-	$	80,035	$	-	$	80,035	$	-	$	113,224	$	-	$	113,224
Long-term investments (held to maturity)	$	-	$	100,079	$	-	$	100,079	$	-	$	216,579	$	-	$	216,579
Contingent consideration	$	-	$	-	$	-	$	-	$	-	$	-	$	-	$	-

	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
	(in thousands)								(in thousands)
Cash and cash equivalents	$	143,583	$	-	$	-	$	143,583	$	184,434	$	-	$	-	$	184,434
Marketable securities	$	85,020	$	-	$	-	$	85,020	$	126,728	$	-	$	-	$	126,728
Short-term investments (held to maturity)	$	-	$	88,480	$	-	$	88,480	$	-	$	57,430	$	-	$	57,430
Long-term investments (held to maturity)	$	-	$	141,981	$	-	$	141,981	$	-	$	246,643	$	-	$	246,643
Contingent consideration	$	-	$	-	$	-	$	-	$	-	$	-	$	-	$	-

This Quarterly Report on Form 10-Q contains certain forward-looking statements within the meaning of Section 27A of the Securities Act of 1933 and Section 21E of the Securities Exchange Act of 1934, and we intend that such forward-looking statements be subject to the safe harbors created thereby. For this purpose, any statements contained in this Quarterly Report on Form 10-Q except for historical information may be deemed to be forward-looking statements. Without limiting the generality of the foregoing, words such as “may,” “will,” “expect,” “believe,” “anticipate,” “intend,” “plan,” “project,” “could,” “estimate,” “target,” “forecast,” or “continue” or the negative of these words or other variations thereof or comparable terminology are intended to identify forward-looking statements. In addition, any statements that refer to projections of our future financial performance, trends in our ~~businesses,~~business, or other characterizations of future events or circumstances are forward-looking statements.

The forward-looking statements included herein are based on current expectations of our management based on available information and involve a number of risks and uncertainties, all of which are difficult or impossible to predict accurately, and many of which are beyond our control. In addition, many of these risks and uncertainties may be exacerbated by the COVID-19 pandemic and any worsening of the global business and economic environment as a result. As such, our actual results may differ materially from those expressed in any forward-looking statements. Readers should carefully review the factors identified in our most recent Annual Report on Form 10-K under the caption “Risk Factors” as well as the additional risks and uncertainties described in other documents we file from time to time with the Securities and Exchange Commission (“SEC”), including ~~our~~this Quarterly Report on Form 10-Q for the quarter ended December 31, ~~2020, this Quarterly Report on Form 10-Q and subsequent quarterly reports on Form 10-Q.~~2021. In light of the significant risks and uncertainties inherent in the forward-looking information included herein, the inclusion of such information should not be regarded as a representation by us or any other person that such results will be achieved, and readers are cautioned not to place undue reliance on such forward-looking information. Except as may be required by law, we disclaim any intent to revise the forward-looking statements contained herein to reflect events or circumstances after the date hereof or to reflect the occurrence of unanticipated events.

Arrowhead Pharmaceuticals, Inc. develops medicines that treat intractable diseases by silencing the genes that cause them. Using a broad portfolio of RNA chemistries and efficient modes of delivery, Arrowhead therapies trigger the RNA interference mechanism to induce rapid, deep and durable knockdown of target genes. RNA interference (“RNAi”) is a mechanism present in living cells that inhibits the expression of a specific gene, thereby affecting the production of a specific protein. Arrowhead’s RNAi-based therapeutics leverage this natural pathway of gene silencing. The Company’s pipeline includes ARO-APOC3 for hypertriglyceridemia, ARO-ANG3 for dyslipidemia, ~~ARO-HSD for liver disease,~~ ARO-ENaC for cystic fibrosis, ARO-HIF2 for renal cell carcinoma, ARO-DUX4 for facioscapulohumeral muscular dystrophy, ~~ARO-LUNG2~~ARO-LUNG2 for chronic obstructive pulmonary disorder, ~~(“COPD”), and~~ ARO-COV for the coronavirus that causes COVID-19 and other possible future pulmonary-borne ~~pathogens.~~pathogens, ARO-C3 for complement mediated diseases and ARO-RAGE and ARO-MUC5AC for various muco-obstructive or inflammatory pulmonary conditions. ARO-~~ARO-JNJ1,~~HSD for liver disease was out-licensed to Glaxosmithkline Intellectual Property (No. 3) Limited (“GSK”) in November 2021. ARO-XDH is being developed for uncontrolled gout under a collaboration agreement with Horizon Therapeutics Ireland DAC (“Horizon”). ARO-JNJ2 and ARO-JNJ3 are being developed for undisclosed liver-expressed targets under a collaboration agreement with Janssen Pharmaceuticals, Inc. (“Janssen”). JNJ-75220795 (ARO-JNJ1) is being developed by Janssen as a potential treatment for patients with non-alcoholic steatohepatitis (NASH). ARO-AAT for liver disease associated with alpha-1 antitrypsin deficiency (“AATD”) was out-licensed to Takeda Pharmaceuticals U.S.A., Inc. (“Takeda”) in October 2020. ~~JNJ3989~~JNJ-3989 (formerly referred to as ARO-HBV) for chronic hepatitis B virus was out-licensed to Janssen in October 2018. Olpasiran (formerly referred to as AMG 890 or ARO-LPA) for cardiovascular disease was out-licensed to Amgen Inc. (“Amgen”) in 2016.

~~Arrowhead has focused its resources on therapeutics that exclusively utilize the Company’s Targeted RNAi Molecule (TRiM~~^TM~~) platform technology. Therapeutics built on the TRiM~~^TM ~~platform have demonstrated high levels of pharmacologic activity in multiple animal models spanning several therapeutic areas. TRiM~~^TM enabled therapeutics offer several potential advantages over prior generation and competing technologies, including: simplified manufacturing and reduced costs; multiple routes of administration including subcutaneous injection and inhaled administration; the ability to target multiple tissue types including liver, lung and tumors; and the potential for improved safety and reduced risk of intracellular buildup, because there are less metabolites from smaller, simpler molecules.

During the first ~~half~~quarter of fiscal ~~year 2021,~~2022, the Company continued to develop and advance its pipeline and partnered ~~candidates. The Company hosted a key opinion leader webinar on~~candidates and expanded its ~~cardiometabolic candidates, ARO-APOC3 and ARO-ANG3. The Company presented positive interim clinical data from AROAAT2002, an open-label Phase 2 clinical study of ARO-AAT,~~facilities to support the Company’s second-generation investigational RNAi therapeutic being developed as a treatment for the rare genetic liver disease associated with AATD. The Company also announced positive clinical data on its cardiometabolic candidates, ARO-APOC3 and ARO-ANG3, at the American Heart Association Scientific Sessions 2020. The Company filed two Investigational New Drug Applications with the United States Food and Drug Administration to begin a Phase 2b clinical study of ARO-APOC3 in patients with severe hypertriglyceridemia and a Phase 2b clinical study of ARO-ANG3 in patients with mixed dyslipidemia. Finally, the Company announced a collaboration with Takeda to co-develop and co-commercialize ARO-AAT for alpha-1 antitrypsin-associated liver disease. See Note 2 of the Notes to Consolidated Financial Statements included in this Quarterly Report on Form 10-Q for more information regarding the collaboration with Takeda.growing pipeline. Several key recent developments include:

Net losses were ~~$26.8~~$62.9 million for the three months ended ~~March~~December 31, 2021 as compared to net losses of ~~$19.8~~$20.7 million for the three months ended ~~March~~December 31, 2020. ~~Net losses were $47.6 million for the six months ended March 31, 2021 as compared to net losses of $22.5 million for the six months ended March 31, 2020.~~ Net losses per share-diluted were ~~$0.26~~$0.60 for the three months ended ~~March~~December 31, 2021 as compared to net losses per share-diluted of $0.20 for the three months ended ~~March 31, 2020. Net losses per share-diluted were $0.46 for the six months ended March 31, 2021 as compared to net losses per share-diluted of $0.23 for the six months ended March~~December 31, 2020. The increase in net losses for the three ~~and six~~ months ended ~~March~~December 31, 2021 was due to an increase in research and development and general and administrative expenses as ~~the~~ Company’s pipeline of candidates has expanded and progressed through clinical trial phases, partially offset by an increase in revenue from the Company’s license and collaboration agreements, primarily from the Takeda ~~collaboration.~~ License Agreement (as defined below) and Horizon License Agreement (as defined below).

The Company has strengthened its liquidity and financial position through upfront and milestone payments received under its collaboration agreements, as well as equity financings. Under the terms of the Company’s agreements with Janssen, taken together, the Company has received $175.0 million as an upfront payment, $75.0 million in the form of an equity investment by JJDC in Arrowhead Common Stock, and ~~two $25.0 million~~four milestone ~~payments.~~payments totaling $70.0 million. Under the terms of the Company’s agreements with Amgen, the Company has received $35.0 million in upfront payments, $21.5 million in the form of an equity investment by Amgen in the Company’s Common Stock and $30.0 million in milestone payments. T~~he Company’s October 2020 licensing agreement with~~The Takeda License Agreement resulted in a $300.0 million upfront payment, and the Horizon License Agreement resulted in a $40.0 million upfront payment. Finally, the GSK License Agreement (as defined below) resulted in an upfront payment of $120.0 million, which was ~~collected~~received in ~~the beginning of the second quarter of 2021.~~January 2022. The Company had ~~$372.4~~$91.6 million of cash and cash equivalents, ~~$125.8~~$126.0 million of marketable securities, ~~$79.1~~$112.5 million in short-term investments, ~~$97.5~~$217.6 million of long term investments and ~~$756.8~~$638.5 million of total assets as of ~~March~~December 31, 2021, as compared to ~~$143.6~~$184.4 million ~~$85.0~~of cash and cash equivalents, $126.7 million ~~$86.9~~of marketable securities, $56.6 million ~~$137.5~~in short-term investments, $245.6 million of long term investments and ~~$522.5~~$710.1 million of total assets as of September 30, ~~2020, respectively.~~2021. Based upon the Company’s current cash and investment resources and operating plan, the Company expects to have sufficient liquidity to fund operations for at least the next twelve months.

There have been no changes to the significant accounting policies disclosed in the Company’s most recent Annual Report on Form 10-K.

The following data summarizes our results of operations for the following periods indicated:

The increase in revenue for the three ~~and six~~ months ended ~~March~~December 31, 2021 compared to the three ~~and six~~ months ended ~~March~~December 31, 2020 was driven by the revenue recognized ~~for~~from the Takeda ~~collaboration.~~License Agreement and the Horizon License Agreement. The increase in net losses during the three ~~and six~~ months ended ~~March~~December 31, 2021 compared to the three ~~and six~~ months ended ~~March~~December 31, 2020 was driven by an increase in research and development and general and administrative expenses as our pipeline of clinical candidates has continued to increase and progress through clinical trial phases, partially offset by an increase in revenue from the Takeda License Agreement and the Horizon License Agreement.

Total revenue for the three months ended ~~March~~December 31, 2021 and 2020 was ~~$32.8~~$27.4 million and ~~$23.5 million, respectively. Total revenue for the six months ended March 31, 2021 and 2020 was $54.1 million and $53.0~~$21.3 million, respectively. Revenue for the three

months ended ~~March~~December 31, 2021 is primarily related to the recognition of ~~$25.4~~$20.8 million of revenue associated with the Takeda License Agreement and the recognition of a portion of the $252.7 million initial transaction price associated with our agreements with Janssen and JJDC for the progress we achieved towards completing our performance obligations under those agreements. Revenue for the six months ended March 31, 2021 is primarily related to the recognition of $33.6$6.7 million of revenue associated with the ~~Takeda~~Horizon License Agreement and the recognition of a portion of the $252.7 million initial transaction price associated with our agreements with Janssen and JJDC for the progress we achieved towards completing our performance obligations under those agreements.Agreement.

On September 28, 2016, the Company entered into two collaboration and license agreements and a common stock purchase agreement with Amgen. Under the Second Collaboration and License Agreement ~~or Olpasiran Agreement,~~(the “Olpasiran Agreement”), Amgen has received a worldwide, exclusive license to Arrowhead’s novel RNAi Olpasiran (previously referred to as AMG 890 or ARO-LPA) program. These RNAi molecules are designed to reduce elevated lipoprotein(a), which is a genetically validated, independent risk factor for atherosclerotic cardiovascular disease. Under the ~~other~~prior collaboration and license agreement (the “First Collaboration and License Agreement” or the “ARO-AMG1 Agreement”), Amgen received an option to a worldwide, exclusive license for ARO-AMG1, an RNAi therapy for an undisclosed genetically validated cardiovascular target. InUnder both agreements, Amgen is wholly responsible for clinical development and commercialization. Under the terms of the agreements taken together, the Company has received $35.0 million in upfront payments, $21.5 million in the form of an equity investment by Amgen in the Company’s Common Stock, and $30.0 million in milestone payments, and may receive up to an additional $400.0 million in remaining development, regulatory and sales milestone payments. The Company is further eligible to receive up to low double-digit royalties for sales of products under the Olpasiran Agreement. In July 2019, Amgen informed the Company that it would not be exercising its option for an exclusive license for ARO-AMG1, and as such, there will be no further milestone or royalty payments under the ARO-AMG1 Agreement.

The Company has evaluated these agreements in accordance with FASB Topics 808 – Collaboration Arrangements and 606 - Revenue for Contracts from Customers. The Company has substantially completed its performance obligations under the Olpasiran Agreement and the ARO-AMG1 Agreement. Future milestones and royalties achieved will be recognized in their entirety when earned. In July 2020, Amgen initiated a Phase 2 clinical study of Olpasiran, which resulted in a $20.0 million milestone payment to the Company. During the three ~~and six~~ months ended ~~March~~December 31, 2021 and 2020, the Company recognized $0 and $0 inof revenue associated with its agreement with Amgen, respectively.As of ~~March~~December 31, 2021, there were $0 in contract assets recorded as accounts receivable and $0 of contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets.

On October 3, 2018, the Company entered into ~~the Janssen~~a License Agreement (the “Janssen License Agreement”) and ~~the Janssen~~a Research Collaboration and Option Agreement (the “Janssen Collaboration Agreement”) with Janssen, part of the Janssen Pharmaceutical Companies of Johnson & Johnson. The Company also entered into a stock purchase agreement with JJDC (“JJDC Stock Purchase Agreement”). Under the Janssen License Agreement, Janssen has received a worldwide, exclusive license to the Company’s JNJ-3989 (ARO-HBV) program, the Company’s third-generation subcutaneously administered RNAi therapeutic candidate being developed as a potential therapy for patients with chronic hepatitis B virus infection. Beyond the Company’s Phase 1/2 study of JNJ-3989 (ARO-HBV), which the Company was responsible for completing, Janssen is ~~also~~ wholly responsible for clinical development and commercialization of JNJ-3989. Under the Janssen Collaboration Agreement, Janssen will be able to select three new targets against which Arrowhead will develop clinical candidates. These candidates are subject to certain restrictions and do not include candidates that already were in the Company’s pipeline. The Company will perform discovery, optimization and preclinical research and development, entirely funded by Janssen, which on its own or in combination with Janssen development work, is sufficient to allow the filing of a U.S. Investigational New Drug Application or equivalent, at which time Janssen will have the option to take an exclusive license. If the option is exercised, Janssen will be wholly responsible for clinical development and commercialization of each optioned candidate. Under the terms of the agreements taken together, the Company has received $175.0 million as an upfront payment, $75.0 million in the form of an equity investment by JJDC in Arrowhead Common Stock under the JJDC Stock Purchase Agreement, and ~~two $25.0~~milestone and option payments totaling $70.0 million, ~~milestone payments,~~ and the Company may receive up to $1.6 billion in development and sales milestones payments for the Janssen License Agreement, and up to $1.9 billion in development and sales milestone payments for the three additional targets covered under the Janssen Collaboration Agreement. The Company is further eligible to receive tiered royalties on product sales up to mid-teens under the Janssen License Agreement and up to low teens under the Janssen Collaboration ~~Agreement on product sales.~~Agreement.

The Company has evaluated these agreements in accordance with FASB ~~Topic~~Topics 808 – Collaboration Arrangements and 606 - Revenue for Contracts from ~~Customers, which became effective for the Company on October 1, 2018.~~Customers. At the inception of these agreements, the Company identified one distinct performance obligation. Regarding the Janssen License Agreement, the Company determined that the key deliverables included the license and certain R&D services including the Company’s responsibility to complete the Phase 1/2 study of JNJ-3989 (ARO-HBV) and the Company’s responsibility to ensure certain manufacturing of JNJ-3989 (ARO-HBV) drug product is completed and delivered to Janssen (the “Janssen R&D Services”). Due to the specialized and unique nature of these Janssen R&D Services and their direct relationship with the license, the Company determined that these deliverables represent one distinct bundle and, thus, one performance obligation. The Company also determined that Janssen’s option to require the Company to develop up to three new targets is not a material right and, thus, not a performance obligation at the onset of the agreement. The consideration for this option is accounted for separately.

The Company determined the transaction price totaled approximately $252.7 million, which includes the upfront payment, the premium paid by JJDC for its equity investment in the Company, ~~the~~ two $25.0 million milestone payments ~~earned~~related to JNJ-3989 (ARO-HBV), and estimated payments for reimbursable Janssen R&D Services to be performed. The Company has allocated the total $252.7 million initial transaction price to its one distinct performance obligation for the JNJ-3989 (ARO-HBV) license and the associated Janssen R&D Services. ~~This revenue~~The Company has recognized this transaction price in its entirety as of September 30, 2021, as its performance obligations were substantially completed. Future milestones and royalties achieved will be recognized ~~using a proportional performance method (based on actual costs incurred versus total estimated costs incurred) beginning~~ in ~~October 2018 and ending as the Company’s efforts in overseeing the Phase 1/2 clinical trial are completed.~~their entirety when earned. During the three months ended ~~March~~December 31, 2021 and 2020, the Company recognized approximately ~~$7.4 million~~$0 and ~~$22.2 million of revenue associated with this performance obligation, respectively. During the six months ended March 31, 2021 and 2020, the Company recognized approximately $20.2 million and $50.9~~$12.7 million of revenue associated with this performance obligation, respectively. As of ~~March~~December 31, 2021, there were ~~$0.6 million~~$0 in contract assets recorded as accounts receivable, and $0 of contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets.

The Company has evaluated the Takeda License Agreement in accordance with FASB ~~Topic~~Topics 808 – Collaborative Arrangements and 606 - Revenue for Contracts from ~~Customers, which became effective for the Company on October 1, 2018.~~Customers. At the inception of the Takeda License Agreement, the Company identified one distinct performance obligation. The Company determined that the key deliverables included the license and certain R&D services including the Company’s responsibilities to complete the initial portion of the SEQUOIA study, to complete the ongoing Phase 2 AROAAT2002 study and to ensure certain manufacturing of ARO-AAT drug product is completed and delivered to Takeda (the “Takeda R&D Services”). Due to the specialized and unique nature of these Takeda R&D Services and their direct relationship with the license, the Company determined that these deliverables represent one distinct bundle and, thus, one performance obligation. Beyond the Takeda R&D Services, which are the responsibility of the Company, Takeda will be responsible for managing future clinical development and ~~commercialization.~~commercialization outside the United States. Within the United States, the Company will also participate in co-development and co-commercialization efforts and will co-fund these efforts with Takeda as part of the 50/50 profit sharing structure within the United States. The Company ~~will co-fund certain~~considers the collaborative activities, including the co-development and co-commercialization, to be a separate unit of ~~the development~~account within Topic 808, and ~~commercialization costs that Takeda manages, and~~as such, these co-funding amounts will be ~~offset against amounts owed to Arrowhead, either from milestones~~recorded as Research and Development Expenses or ~~royalties earned, or profits earned under the 50/50 profit sharing structure for U.S. commercialization.~~General and Administrative Expenses, as appropriate.

The Company determined the initial transaction price totaled ~~approximately~~ $300.0 million, which includes the upfront payment. The Company ~~will exclude~~has excluded any future ~~estimated~~ milestones ~~royalties,~~ or ~~profit-sharing payments~~royalties from this transaction price to date. The Company ~~will allocate~~has allocated the total $300.0 million initial transaction price to its one distinct performance obligation for the ARO-AAT license and the associated Takeda R&D Services. Revenue will be recognized using a proportional performance method (based on actual ~~costs incurred~~patient visits completed versus total estimated ~~costs incurred~~visits completed for the ~~Takeda R&D Services)~~ongoing SEQUOIA and AROAAT2002 clinical studies). Revenue for the three months ended ~~March~~December 31, 2021 and 2020 ~~were $25.4~~was $20.8 million and ~~$0, respectively. Revenue for the six months ended March 31, 2021 and 2020 were $33.6 million and $0,~~$8.2, respectively. As of ~~March~~December 31, 2021, there were $0 in contract assets recorded as accounts receivable, ~~$144.9~~$82.0 million in contract liabilities recorded as deferred revenue and ~~$121.5~~$106.5 million in contract liabilities recorded as deferred revenue, net of the current ~~portion. See Note 2~~portion, and $2.9 million in contract liabilities recorded as accrued expenses. The $2.9 million in accrued expenses was primarily driven by co-development and co-commercialization activities.

The Company has evaluated the Horizon License Agreement in accordance with FASB Topics 808 – Collaborative Arrangements and 606 - Revenue for Contracts from Customers. At the inception of the Horizon License Agreement, the Company identified one distinct performance obligation. The Company determined that the key deliverables included the license and certain R&D services, including the Company’s responsibilities to conduct all activities through the preclinical stages of development of ARO-XDH (the “Horizon R&D Services”). Due to the ~~Notes~~specialized and unique nature of these Horizon R&D Services and their direct relationship with the license, the Company determined that these deliverables represented one distinct bundle and, thus, one performance obligation. Beyond the Horizon R&D Services, which are the responsibility of the Company, Horizon will be responsible for managing future clinical development and commercialization of ARO-XDH.

The Company determined the initial transaction price totaled $40.0 million, including the upfront payment. The Company has excluded any future estimated milestones or royalties, from this transaction price to ~~Consolidated Financial Statements~~date. The Company will allocate the total $40.0 million initial transaction price to its one distinct performance obligation for the ARO-XDH license and the associated Horizon R&D Services. Revenue will be recognized on a straight-line basis over the estimated timeframe for completing the Horizon R&D Services. The Company determined that the straight-line basis was appropriate as its efforts will be expended evenly over the course of completing its performance obligation. Revenue for the three months ended December 31, 2021 and 2020 was $6.7 million and $0, respectively. As of December 31, 2021, there were $0.1 million in contract assets recorded as accounts receivable, $26.7 million in contract liabilities recorded as deferred revenue.

nonalcoholic steatohepatitis (NASH). The exclusive license is worldwide with the exception of greater China, for which the Company will retain rights to develop and commercialize. Beyond the Company’s Phase 1/2 study of (ARO-HSD), which the Company is responsible for completing, GSK is wholly responsible for clinical development and commercialization of ARO-HSD in its territory. Under the terms of the agreement, the Company has received an upfront payment of $120 million and is eligible for additional payments of $30 million at the start of Phase 2 and $100 million upon achieving a successful Phase 2 trial readout and the first patient dosed in a Phase 3 trial. Furthermore, should the Phase 3 trial read out positively, and the potential new medicine receives regulatory approval in major markets, the deal provides for commercial milestone payments to the Company of up to $190 million at first commercial sale, and up to $590 million in sales-related milestone payments. The Company is further eligible to receive tiered royalties on net product sales in a range of mid-teens to twenty percent.

The Company has evaluated the GSK License Agreement in accordance with FASB Topics 808 – Collaborative Arrangements and 606 - Revenue for Contracts from Customers. At the inception of the GSK License Agreement, the Company identified one distinct performance obligation. The Company determined that the key deliverables included the license and certain R&D services, including the Company’s responsibility to complete the Phase 1/2 study, (the “GSK R&D Services”). Due to the specialized and unique nature of these GSK R&D Services and their direct relationship with the license, the Company determined that these deliverables represented one distinct bundle and, thus, one performance obligation. Beyond the GSK R&D Services, which are the responsibility of the Company, GSK will be responsible for managing future clinical development and commercialization in its territory.

The Company determined the initial transaction price totaled $120.0 million, including the upfront payment. The Company has excluded any future estimated milestones or royalties from this ~~Quarterly Report on Form 10-Q~~transaction price to date. The Company has allocated the total $120.0 million initial transaction price to its one distinct performance obligation for ~~more information regarding our collaboration~~the ARO-HSD license and ~~license agreements.~~the associated GSK R&D Services. Revenue will be recognized using a proportional performance method. As of December 31, 2021, no revenue or contract assets or liabilities were recognized as the GSK License Agreement had not yet completed customary closing conditions, including clearance by the relevant competition authorities. This clearance was achieved in January 2022 and the upfront payment of $120.0 million was also received by the Company in January 2022.

The analysis below details the operating expenses and discusses the expenditures of the Company within the major expense categories. Certain reclassifications have been made to prior-period operating expense categories to conform to the current period presentation. For purposes of comparison, the amounts for the three ~~and six~~ months ended ~~March~~December 31, 2021 and 2020 are shown in the tables below.

R&D expenses are related to the Company’s research and development efforts and related program costs, which are comprised primarily of outsourced costs related to the manufacturing of clinical supplies, toxicity/efficacy studies and clinical trial expenses. Internal costs primarily relate to operations at our research facilities in Madison, Wisconsin and San Diego, California, including facility costs and laboratory-related expenses. Salaries and stock compensation expense consist of salary, bonuses, payroll taxes and related benefits and stock compensation for our R&D personnel. Depreciation and amortization expense ~~relates to~~consist of depreciation on lab equipment and leasehold improvements at our research facilities. We do not separately track R&D expenses by individual research and development projects, including by individual drug candidates. The Company operates in a cross-functional manner across projects and does not separately allocate facilities-related costs, candidate costs, discovery costs, compensation

expenses, depreciation and amortization expenses, and other expenses for research and development activities. The following table provides details of research and development expenses for the periods indicated:

	Six					Six										Three					Three
	Months Ended		% of Expense			Months Ended		% of Expense			Increase (Decrease)					Months Ended		% of Expense			Months Ended		% of Expense			Increase (Decrease)
	March 31, 2021		Category			March 31, 2020		Category			$		%			December 31, 2021		Category			December 31, 2020		Category			$		%
Salaries	$	16,857		21	%	$	8,312		16	%	$	8,545		103	%	$	10,994		17	%	$	8,173		22	%	$	2,821		35	%
Facilities related		3,150		4	%		1,444		3	%		1,706		118	%		2,038		3	%		1,478		4	%		560		38	%
Candidate costs		35,684		44	%		29,145		55	%		6,539		22	%		32,345		49	%		15,017		41	%		17,328		115	%
R&D discovery costs		10,213		13	%		7,471		14	%		2,742		37	%		11,000		17	%		4,711		13	%		6,289		133	%
Total research and development expense, excluding non-cash expense	$	65,904		81	%	$	46,372		88	%	$	19,532		42	%		56,377		86	%		29,379		80	%		26,998		92	%
Stock compensation		11,891		15	%		4,115		8	%		7,776		189	%		7,218		11	%		5,486		15	%		1,732		32	%
Depreciation/amortization		3,456		4	%		2,330		4	%		1,126		48	%		2,170		3	%		1,690		5	%		480		28	%
Total research and development expense	$	81,251		100	%	$	52,817		100	%	$	28,434		54	%	$	65,765		100	%	$	36,555		100	%	$	29,210		80	%

Salaries expense increased by ~~$4,469,000~~$2,821,000 from ~~$4,216,000~~$8,173,000 during the three months ended ~~March~~December 31, 2020 to ~~$8,685,000 during the current period. Salaries expense increased by $8,545,000 from $8,312,000 during the six months ended March 31, 2020 to $16,857,000~~$10,994,000 during the current period. This increase is primarily due to an increase in R&D headcount that has occurred as the Company has expanded its pipeline of candidates. We anticipate this expense to continue to increase as we continue to expand our pipeline of candidates and increase headcount to support our discovery efforts to identify new drug candidates.

Facilities expense increased by ~~$848,000~~$560,000 from ~~$823,000~~$1,478,000 during the three months ended ~~March~~December 31, 2020 to ~~$1,671,000 during the current period. Facilities expense increased by $1,706,000 from $1,444,000 during the six months ended March 31, 2020 to $3,150,000~~$2,038,000 during the current period. This category includes rental costs for our research and development facilities in Madison, Wisconsin and San Diego, California. ~~This~~We expect this expense to continue to increase ~~is primarily due~~as we continue to ~~the commencement of~~build out our ~~sublease in San Diego, California in April 2020.~~manufacturing capabilities to support our discovery efforts to identify new drug candidates.

Candidate costs increased by ~~$4,951,000~~$17,328,000 from ~~$15,716,000~~$15,017,000 during the three months ended ~~March~~December 31, 2020 to ~~$20,667,000 during the current period. Candidate costs increased by $6,539,000 from $29,145,000 during the six months ended March 31, 2020 to $35,684,000~~$32,345,000 during the current period. This increase is primarily due to the progression of our pipeline of candidates into and through clinical trials, which results in higher outsourced clinical trial, toxicity study and manufacturing costs. For example, our cardiometabolic candidates, ARO-ANG3 and ARO-APOC3, have advanced into phase 2 and phase 3 clinical trials. We anticipate these expenses to continue to increase as our pipeline of candidates grows and progresses to later phase clinical trials.

R&D discovery costs increased by ~~$986,000~~$6,289,000 from ~~$4,516,000~~$4,711,000 during the three months ended ~~March~~December 31, 2020 to ~~$5,502,000 in the current period. R&D discovery costs increased by $2,742,000 from $7,471,000 during the six months ended March 31, 2020 to $10,213,000~~$11,000,000 in the current period. This increase is primarily due to the growth of our discovery efforts, including the addition of our research facility in San Diego. We anticipate this expense to continue to increase as we increase headcount to support our discovery efforts to identify new drug candidates.

Stock compensation expense, a non-cash expense, increased by ~~$3,453,000~~$1,732,000 from ~~$2,953,000~~$5,486,000 during the three months ended ~~March~~December 31, 2020 to ~~$6,406,000 during the current period. Stock compensation expense, a non-cash expense, increased by $7,776,000 from $4,115,000 during the six months ended March 31, 2020 to $11,891,000~~$7,218,000 during the current period. Stock compensation expense is based upon the valuation of stock options and restricted stock units granted to employees, directors and certain consultants. Many variables affect the amount expensed, including the Company’s stock price on the date of the grant, as well as other assumptions. The increase in the expense in the current period is primarily due to the increased headcount discussed above and a mix of higher grant date fair values of awards amortizing during the current period due to the Company’s stock price at the time of the grants. We generally expect future stock compensation expense to continue to increase as our headcount continues to increase to support our clinical pipeline.

Depreciation and amortization expense, a non-cash expense, increased by ~~$547,000~~$480,000 from ~~$1,219,000~~$1,690,000 during the three months ended ~~March~~December 31, 2020 to ~~$1,766,000 during the current period. Depreciation and amortization expense, a non-cash expense, increased by $1,126,000 from $2,330,000 during the six months ended March 31, 2020 to $3,456,000~~$2,170,000 during the current period. The majority of depreciation and amortization expense relates to depreciation on lab equipment and leasehold improvements at our Madison and San Diego research ~~facility.~~facilities. The increase in depreciation and amortization expense is due to an increase in laboratory equipment and leasehold improvements. We expect this amount to increase in the future as we continue to purchase additional lab equipment to support our growing pipeline.

The following table provides details of our general and administrative expenses for the periods indicated:

	Three					Three											Three					Three
	Months Ended		% of Expense			Months Ended		% of Expense			Increase (Decrease)						Months Ended		% of Expense			Months Ended		% of Expense			Increase (Decrease)
	March 31, 2021		Category			March 31, 2020		Category			$			%			December 31, 2021		Category			December 31, 2020		Category			$		%
Salaries	$	3,257		20	%	$	3,033		19	%	$	224			7	%	$	3,430		14	%	$	2,584		29	%	$	846		33	%
Professional/outside services		1,838		11	%		1,677		10	%		161			10	%		2,177		9	%		1,982		23	%		195		10	%
Facilities related		787		5	%		418		3	%		369			88	%		680		3	%		421		5	%		259		62	%
Other G&A		1,355		8	%		1,026		6	%		329			32	%		1,018		4	%		1,003		11	%		15		1	%
Total general & administrative expense, excluding non-cash expense		7,237		44	%		6,154		38	%		1,083			137	%		7,305		29	%		5,990		68	%		1,315		22	%
Stock compensation		8,953		55	%		10,019		61	%		(1,066	)		-11	%		17,287		69	%		2,658		30	%		14,629		550	%
Depreciation/amortization		156		1	%		153		1	%		3			2	%		403		2	%		154		2	%		249		162	%
Total general & administrative expense	$	16,346		100	%	$	16,326		100	%	$	20			129	%	$	24,995		100	%	$	8,802		100	%	$	16,193		184	%

Salaries expense increased by ~~$224,000~~$846,000 from ~~$3,033,000~~$2,584,000 during the three months ended ~~March~~December 31, 2020 to ~~$3,257,000~~$3,430,000 during the current period. ~~Salaries expense decreased by $1,273,000 from $7,114,000 during the six months ended March 31, 2020 to $5,841,000 during the current period. The~~This increase ~~of $224,000 during the three months ended March 31, 2021 as compared to the three months ended March 31, 2020~~ is primarily due to an increase in ~~headcount. The decrease of $1,273,000 during~~G&A headcount that has occurred as the ~~six months ended March 31, 2021 as compared to the six months ended March 31, 2020 is primarily due to higher annual performance bonuses awarded in December 2019.~~Company has grown. We expect salaries expense to continue to increase as our headcount continues to increase to support our expanding clinical pipeline.

Professional/outside services include legal, accounting, consulting, patent expenses, business insurance expenses and other outside services retained by the Company. Professional/outside services expense increased by ~~$161,000~~$195,000 from ~~$1,677,000~~$1,982,000 during the three months ended ~~March~~December 31, 2020 to ~~$1,838,000 during the current period. Professional/outside services expense increased by $321,000 from $3,499,000 during the six months ended March 31, 2020 to $3,820,000~~$2,177,000 during the current period. The increase in professional/outside services expense is primarily related to ~~increased consulting costs.~~the timing of certain patent-related expenses.

Facilities-related expense increased by ~~$369,000~~$259,000 from ~~$418,000~~$421,000 during the three months ended ~~March~~December 31, 2020 to ~~$787,000 during the current period. Facilities-related expense increased by $306,000 from $1,211,000 during the six months ended March 31, 2020 to $1,517,000~~$680,000 during the current period. This category primarily includes rental costs for our corporate headquarters in Pasadena, California. ~~The~~We expect future facilities-related expense to increase ~~is due~~as we continue to ~~increased communication and technology costs as the Company’s~~increase our headcount ~~continues~~ to ~~grow.~~support our discovery efforts.

Other G&A expense increased by ~~$329,000~~$15,000 from ~~$1,026,000~~$1,003,000 during the three months ended ~~March~~December 31, 2020 to ~~$1,355,000 during the current period. Other G&A expense increased by $263,000 from $1,785,000 during the six months ended March 31, 2020 to $2,048,000~~$1,018,000 during the current period. This category consists primarily of travel, communication and technology, office expenses, and franchise and property tax expenses. The increase is due to ~~an increase in headcount at~~increased information technology costs to support the Company’s ~~corporate headquarters.~~increased headcount.

Stock compensation expense, a non-cash expense, ~~decreased~~increased by ~~$1,066,000~~$14,629,000 from ~~$10,019,000~~$2,658,000 during the three months ended ~~March~~December 31, 2020 to ~~$8,953,000 during the current period. Stock compensation expense, a non-cash expense, decreased by $1,738,000 from $13,349,000 during the six months ended March 31, 2020 to $11,611,000~~$17,287,000 during the current period. Stock compensation expense is based upon the valuation of stock options and restricted stock units granted to employees, directors and certain consultants. Many variables affect the amount expensed, including the Company’s stock price on the date of the grant, as well as other assumptions. The increase in the current period is due to a performance award that was achieved earlier than anticipated, as well as a modification of certain performance awards to include market conditions. The fair value of market condition-based awards is expensed ratably over the service period and is not adjusted for actual achievement.We generally expect future stock compensation expense to continue to increase as our headcount continues to increase to support our clinical pipeline.

Depreciation and amortization expense, a noncash expense, increased by ~~$3,000~~$249,000 from ~~$153,000~~$154,000 during the three months ended ~~March~~December 31, 2020 to ~~$156,000 during the current period. Depreciation and amortization expense, a noncash expense, increased by $8,000 from $302,000 during the six months ended March 31, 2020 to $310,000~~$403,000 during the current period. The increase is primarily related to amortization of leasehold improvements for our corporate headquarters.

Other income/expense was ~~income of $2,405,000~~$3,322,000 during the three months ended ~~March~~December 31, 2020 compared to ~~income of $1,414,000 during the current period. Other income/expense was income of $4,585,000 during the six months ended March 31, 2020 compared to income of $4,735,000~~$449,000 during the current period. Other income is primarily related to interest income and realized and unrealized gain/loss on our marketable securities. The decrease in other income/expense is due to lower yields on more recently purchased bonds.

Arrowhead has historically financed its operations through the sale of its equity ~~securities.~~securities and revenue from its collaboration agreements. Research and development activities have required significant capital investment since the Company’s inception and are expected to continue to require significant cash expenditure as the Company’s pipeline continues to expand and matures into later stage clinical trials. Additionally, the Company’s plans to expand its facilities with its purchase of land in Verona, Wisconsin, and its entry into a new lease in San Diego, California. Each of these expansions is designed to increase the ~~future.~~Company’s internal manufacturing and discovery capabilities, and each will require significant capital investment.

At ~~March~~December 31, 2021, the Company had cash on hand of approximately ~~$372.4~~$91.6 million as compared to ~~$143.6~~$184.4 million at September 30, ~~2020.~~2021. Cash invested in short-term fixed income securities and marketable securities was ~~$204.9~~$238.5 million at ~~March~~December 31, 2021, compared to ~~$171.9~~$183.4 million at September 30, ~~2020.~~2021. Cash invested in long-term fixed income securities was ~~$97.5~~$217.6 million at ~~March~~December 31, 2021, compared to ~~$137.5~~$245.6 million at September 30, ~~2020.~~2021. The Company also entered into an Open Market Sale Agreement (the “ATM ~~agreement”~~Agreement”) in August 2020, pursuant to which the Company may, from time to time, sell up to $250,000,000 in shares of the Company’s Common Stock through Jefferies LLC. As of ~~March~~December 31, 2021, no shares have been ~~issued~~sold under the ATM ~~agreement.~~Agreement. The Company believes its current financial resources are sufficient to fund its operations through at least the next twelve months.

A summary of cash flows for the ~~six~~three months ended ~~March~~December 31, 2021 and 2020 is as follows:

During the ~~six~~three months ended ~~March~~December 31, 2021, cash flow ~~provided~~used by operating activities was ~~$225.0~~$61.3 million, which was primarily due to ~~the $300 million payment received under the Takeda License Agreement, partially offset by~~ ongoing expenses ofrelated to the Company’s research and development programs and general and administrative expenses. Cash used in investing activities was ~~$3.9~~$33.4 million, which was primarily related to the purchase of property and equipment of ~~$11.4~~$5.8 million ~~partially offset by the~~ and net ~~sales~~purchase of investments of ~~$7.5~~ $27.6 million. Cash provided by financing activities of ~~$7.7~~$1.9 million was related to cash received from stock option exercises.

During the ~~six~~three months ended ~~March~~December 31, 2020, the Company used ~~$51.1~~$38.9 million in cash from operating activities, which was primarily related to the ongoing expenses of the Company’s research and development programs and general and administrative expenses. Cash ~~used~~provided in investing activities was ~~$168.8~~$30.2 million, which was primarily related to the ~~purchase~~sale of ~~fixed-income investments~~marketable securities of ~~$180.5 million and property and equipment of $7.9~~$34.4 million, partially offset by the ~~maturity~~purchase of ~~$19.6 million~~property and equipment of ~~fixed-income securities.~~$4.3 million. Cash provided by financing activities of ~~$254.8~~$5.1 million was ~~driven by the Company’s securities financing in December 2019, which generated $250.5 million in net cash proceeds, as well as $4.3 million in~~related to cash received from stock option exercises.

~~We do~~On December 20, 2021, the Company completed a purchase of 13 acres of land in the Verona Technology Park in Verona, WI, which is planned to be the site of an approximately 140,000 square foot drug manufacturing facility and an approximately 115,000 square foot laboratory and office facility to support process development and analytical activities. Arrowhead intends to invest between $200 million and $250 million into the buildout of the facilities. As part of this acquisition, the Company also entered into a development agreement with the City of Verona to construct certain infrastructure improvements within the TIF district, and will be reimbursed by the City of Verona by future tax increment revenue generated from the developed property. The total amount of funding that City of Verona will pay as reimbursements under the TIF program for these improvements is not ~~have any off-balance sheet arrangements.~~guaranteed and will depend on future tax revenues generated from the developed property.

There has been no material change in our exposure to market risk from that described in Item 7A of our Annual Report on Form 10-K for the year ended September 30, ~~2020.~~2021.

Our Chief Executive Officer and our Chief Financial Officer, after evaluating our “disclosure controls and procedures” (as defined in Rules 13a-15(e) and 15d-15(e) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”)) as of the end of the period covered by this Quarterly Report on Form 10-Q (the “Evaluation Date”), have concluded that, as of the Evaluation Date, our disclosure controls and procedures are effective to ensure that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in ~~SEC~~Securities and Exchange Commission rules and forms, and to ensure that information required to be disclosed by us in such reports is accumulated and communicated to our management, including our Chief Executive Officer and Chief Financial Officer where appropriate, to allow timely decisions regarding required disclosure.

No change in the Company’s internal controls over financial reporting (as defined in ~~Rule~~Rules 13a-15(f) and 15d-15(f) of the Exchange Act) occurred during the Company’s most recent fiscal quarter that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

From time to time, we may be involved in routine legal proceedings, as well as demands, claims and threatened litigation, which arise in the normal course of our business. Litigation can be expensive and disruptive to normal business operations. Moreover, the results of legal proceedings, particularly complex legal proceedings, cannot be predicted with any certainty. ~~We disclosed information about certain of our~~There have been no material developments in the legal proceedings that we disclosed in Part I, Item 3 of our Annual Report on Form 10-K for the year ended September 30, ~~2020.~~2021.

There have been no material changes to the risk factors included in our Annual Report on Form 10-K for the year ended September 30, ~~2020.~~2021. Please carefully consider the information set forth in this Quarterly Report on Form 10-Q and the risk factors discussed in Part I, “Item 1A. Risk Factors” in our Annual Report on Form 10-K for the year ended September 30, ~~2020,~~2021, which could materially affect our business, financial condition or future results. The risks described in our Annual Report on Form 10-K, as well as other risks and uncertainties, could materially and adversely affect our business, results of operations and financial condition, which in turn could materially and adversely affect the trading price of shares of our Common Stock. Additional risks not currently known or currently material to us may also harm our business.

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this Quarterly Report on Form 10-Q to be signed on its behalf by the undersigned, thereunto duly authorized.

Delaware		46-0408024
(State or other jurisdiction of ~~incorporation)~~incorporation or organization)		(I.R.S. Employer Identification No.)

Title of each class		Trading Symbol(s)		Name of each exchange on which registered
Common Stock, ~~Par Value~~par value $0.001 per share		ARWR		The Nasdaq Global Select Market

	Page(s)
PART I — FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS	1

Consolidated Balance Sheets	1

Consolidated Statements of Operations and Comprehensive Income (Loss)	2

Consolidated Statements of Stockholders’ Equity	3

Consolidated Statements of Cash Flows	4

Notes to Consolidated Financial Statements	5

ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS	1617

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK	2526

ITEM 4. CONTROLS AND PROCEDURES	2526

PART II — OTHER INFORMATION	2627

ITEM 1. LEGAL PROCEEDINGS	2627

ITEM 1A. RISK FACTORS	2627

ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS	2627

ITEM 3. DEFAULTS UPON SENIOR SECURITIES	2627

ITEM 4. MINE SAFETY DISCLOSURES	2627

ITEM 5. OTHER INFORMATION	2627

ITEM 6. EXHIBITS	2728

SIGNATURE	2829

Exhibit Number		Document Description

~~10.1~~10.1*†		Collaboration and License Agreement by and between Arrowhead Pharmaceuticals, Inc. and Glaxosmithkline Intellectual Property, dated November 22, 2021 ~~Incentive Plan (Incorporated by reference from Exhibit A of the Company’s Definitive Proxy Statement on Schedule 14A filed on January 28, 2021)~~
	~~31.1~~
10.2*†		Lease Agreement by and between Arrowhead Pharmaceuticals, Inc. and ARE-SD Region No. 72, LLC, dated November 19, 2021.

10.3		Form of RSU Agreement for Officers and Certain Other Employees (Arrowhead Pharmaceuticals, Inc. 2021 Incentive Plan- Inducement Award) (incorporated by reference from Exhibit 99.1 of the Company’s Form S-8 filed on December 22, 2021).
10.4		Form of RSU Agreement for Employees (Arrowhead Pharmaceuticals, Inc. 2021 Incentive Plan- Inducement Award) (incorporated by reference from Exhibit 99.2 of the Company’s Form S-8 filed on December 22, 2021).
10.5		Form of Stock Option Grant (Arrowhead Pharmaceuticals, Inc. 2021 Incentive Plan- Inducement Award) (incorporated by reference from Exhibit 99.3 of the Company’s Form S-8 filed on December 22, 2021).

10.6† 31.1		Separation and Release of Claims Agreement between Arrowhead Pharmaceuticals, Inc. and James Hassard Certification of Chief Executive Officer pursuant to Rule 13a-14(a) of the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002*2002

~~31.2~~31.2*		Certification of Chief Financial Officer pursuant to Rule 13a-14(a) of the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002*2002

~~32.1~~32.1**		Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002**2002

~~32.2~~32.2**		Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002**2002

~~101.INS~~ ~~101.SCH~~101.INS*		Inline XBRL Instance Document Inline XBRL Taxonomy Extension Schema Document*

~~101.CAL~~101.SCH*		Inline XBRL Taxonomy Extension Schema Document

101.CAL*		Inline XBRL Taxonomy Extension Calculation Linkbase Document*Document

~~101.LAB~~101.LAB*		Inline XBRL Taxonomy Extension Label Linkbase Document*Document

~~101.PRE~~101.PRE*		Inline XBRL Taxonomy Extension Presentation Linkbase Document*Document

~~101.DEF~~101.DEF*		Inline XBRL Taxonomy Extension Definition Linkbase Document*Document

~~104~~104*		The cover page from this Quarterly Report on Form 10-Q, formatted in Inline XBRL (included as Exhibit 101)*

	ARROWHEAD PHARMACEUTICALS, INC.

	By:		/s/ Kenneth A. Myszkowski
			Kenneth A. Myszkowski Chief Financial Officer
			(Principal Financial Officer and Duly Authorized Officer)

	Six Months Ended			Six Months Ended
	March 31, 2021			March 31, 2020
	(in thousands)
Cash Flow from:
Operating Activities		224,951			(51,115	)
Investing Activities		(3,892	)		(168,849	)
Financing Activities		7,735			254,811
Net Increase (decrease) in cash and cash equivalents		228,794			34,847
Cash and cash equivalents at beginning of period		143,583			221,804
Cash and cash equivalents at end of period		372,377			256,651

	Three Months Ended			Three Months Ended
	December 31, 2021			December 31, 2020
	(in thousands)
Cash flow from:
Operating activities		(61,347	)		(38,922	)
Investing activities		(33,385	)		30,158
Financing activities		1,885			5,102
Net increase (decrease) in cash and cash equivalents		(92,847	)		(3,662	)
Cash and cash equivalents at beginning of period		184,434			143,583
Cash and cash equivalents at end of period		91,587			139,921

Large Accelerated Filer

Accelerated Filer

Non-Accelerated Filer

Smaller Reporting Company

Emerging Growth Company