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”, “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 ~~May 5,~~July 27, 2020 was ~~101,773,274.~~102,291,803.

	(unaudited) March 31, 2020			September 30, 2019			(unaudited) June 30, 2020			September 30, 2019
ASSETS
CURRENT ASSETS
Cash and cash equivalents	$	256,650,727		$	221,804,128		$	219,322,617		$	221,804,128
Accounts receivable		1,265,771			661,361			21,692,564			661,361
Prepaid expenses		3,062,333			3,317,999			4,096,473			3,317,999
Other current assets		2,536,284			2,563,435			2,411,937			2,563,435
Short term investments		50,959,058			36,899,894			67,709,263			36,899,894
TOTAL CURRENT ASSETS		314,474,173			265,246,817			315,232,854			265,246,817
Property and equipment, net		29,362,741			23,214,899			30,389,707			23,214,899
Intangible assets, net		16,213,366			17,063,580			15,788,258			17,063,580
Long term investments		190,618,075			44,175,993			177,529,881			44,175,993
Right-of-use assets		10,263,197			-			16,522,013			-
Other assets		144,150			144,148			265,359			144,148
TOTAL ASSETS	$	561,075,702		$	349,845,437		$	555,728,072		$	349,845,437
LIABILITIES AND STOCKHOLDERS’ EQUITY
CURRENT LIABILITIES
Accounts payable	$	13,417,692		$	7,649,921		$	4,073,869		$	7,649,921
Accrued expenses		4,419,233			6,504,729			9,414,696			6,504,729
Accrued payroll and benefits		1,616,090			4,955,887			1,991,001			4,955,887
Lease liabilities		688,454			-			1,011,951			-
Deferred rent		-			173,952			-			173,952
Deferred revenue		33,174,765			77,769,629			26,274,362			77,769,629
Other current liabilities		17,263			16,561			17,262			16,561
TOTAL CURRENT LIABILITIES		53,333,497			97,070,679			42,783,141			97,070,679
LONG-TERM LIABILITIES
Lease liabilities, net of current portion		14,178,735			-			20,359,726			-
Deferred rent, net of current portion		-			3,703,364			-			3,703,364
Deferred revenue, net of current portion		-			5,035,142			-			5,035,142
TOTAL LONG-TERM LIABILITIES		14,178,735			8,738,506			20,359,726			8,738,506
Commitments and contingencies (Note 7)
STOCKHOLDERS’ EQUITY
Arrowhead Pharmaceuticals, Inc. stockholders' equity:
Common stock, $0.001 par value; 145,000,000 shares authorized; 101,748,107 and 95,506,271 shares issued and outstanding as of March 31, 2020 and September 30, 2019, respectively		194,117			187,876
Common stock, $0.001 par value; 145,000,000 shares authorized; 102,250,872 and 95,506,271 shares issued and outstanding as of June 30, 2020 and September 30, 2019, respectively								194,620			187,876
Additional paid-in capital		936,353,920			664,086,155			948,532,470			664,086,155
Accumulated other comprehensive income (loss)		(629,114	)		(391,624	)		(175,219	)		(391,624	)
Accumulated deficit		(441,800,265	)		(419,290,967	)		(455,411,478	)		(419,290,967	)
Total Arrowhead Pharmaceuticals, Inc. stockholders' equity		494,118,658			244,591,440			493,140,393			244,591,440
Noncontrolling interest		(555,188	)		(555,188	)		(555,188	)		(555,188	)
TOTAL STOCKHOLDERS’ EQUITY		493,563,470			244,036,252			492,585,205			244,036,252
TOTAL LIABILITIES AND STOCKHOLDERS’ EQUITY	$	561,075,702		$	349,845,437		$	555,728,072		$	349,845,437

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 June 30,						Nine Months Ended June 30,
	2020			2019			2020			2019			2020			2019			2020			2019
REVENUE	$	23,528,853		$	48,148,275		$	52,983,433		$	82,806,171		$	27,375,778		$	42,696,636		$	80,359,211		$	125,502,807
OPERATING EXPENSES
Research and development		29,443,335			20,798,628			52,816,951			38,370,671			32,573,134			19,291,710			85,390,086			57,662,381
General and administrative expenses		16,325,773			5,338,955			27,260,330			11,478,664			10,748,506			4,809,177			38,008,836			16,287,841
TOTAL OPERATING EXPENSES		45,769,108			26,137,583			80,077,281			49,849,335			43,321,640			24,100,887			123,398,922			73,950,222
OPERATING INCOME (LOSS)		(22,240,255	)		22,010,692			(27,093,848	)		32,956,836			(15,945,862	)		18,595,749			(43,039,711	)		51,552,585
OTHER INCOME (EXPENSE)
Interest income (expense), net		2,404,685			1,886,290			4,584,550			2,977,399			2,334,649			1,739,959			6,919,200			4,717,359
TOTAL OTHER INCOME (EXPENSE)		2,404,685			1,886,290			4,584,550			2,977,399			2,334,649			1,739,959			6,919,200			4,717,359
INCOME (LOSS) BEFORE INCOME TAXES		(19,835,570	)		23,896,982			(22,509,298	)		35,934,235			(13,611,213	)		20,335,708			(36,120,511	)		56,269,944
Provision for income taxes		-			-			-			-			-			-			-			-
NET INCOME (LOSS)		(19,835,570	)		23,896,982			(22,509,298	)		35,934,235			(13,611,213	)		20,335,708			(36,120,511	)		56,269,944
NET INCOME (LOSS) PER SHARE - BASIC	$	(0.20	)	$	0.25		$	(0.23	)	$	0.39		$	(0.13	)	$	0.21		$	(0.36	)	$	0.60
NET INCOME (LOSS) PER SHARE - DILUTED	$	(0.20	)	$	0.24		$	(0.23	)	$	0.37		$	(0.13	)	$	0.21		$	(0.36	)	$	0.58
Weighted average shares outstanding - basic		101,653,136			94,155,407			99,359,140			92,623,615			101,843,436			94,935,471			100,184,216			93,364,102
Weighted average shares outstanding - diluted		101,653,136			98,082,644			99,359,140			97,214,546			101,843,436			98,884,744			100,184,216			97,814,019
OTHER COMPREHENSIVE INCOME (LOSS), NET OF TAX:
Foreign currency translation adjustments		(433,564	)		(28,162	)		(237,490	)		(50,342	)		453,895			(31,172	)		216,405			(81,514	)
COMPREHENSIVE INCOME (LOSS)	$	(20,269,134	)	$	23,868,820		$	(22,746,788	)	$	35,883,893		$	(13,157,318	)	$	20,304,536		$	(35,904,106	)	$	56,188,430

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

	Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals			Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals
Balance at December 31, 2018		92,591,457	$	184,961	$	647,142,565		$	(43,744	)	$	(475,228,563	)	$	(555,188	)	$	171,500,031
Balance at March 31, 2019																					94,665,718	$	187,035	$	652,411,876		$	(71,906	)	$	(451,331,580	)	$	(555,188	)	$	200,640,237
Stock-based compensation																					-		-		1,957,993			-			-			-			1,957,993
Exercise of stock options																					541,919		542		2,766,732			-			-			-			2,767,274
Foreign currency translation adjustments																					-		-		-			(31,172	)		-			-			(31,172	)
Net income (loss) for the three months ended June 30, 2019																					-		-		-			-			20,335,708			-			20,335,708
Balance at June 30, 2019																					95,207,637	$	187,577	$	657,136,601		$	(103,078	)	$	(430,995,872	)	$	(555,188	)	$	225,670,040

																				Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals
Balance at March 31, 2020																					101,748,107	$	194,117	$	936,353,920		$	(629,114	)	$	(441,800,265	)	$	(555,188	)	$	493,563,470
Stock-based compensation		-		-		2,601,348			-			-			-			2,601,348			-		-		10,046,208			-			-			-			10,046,208
Exercise of stock options		535,915		536		2,669,501			-			-			-			2,670,037			302,765		303		2,132,542			-			-			-			2,132,845
Common stock - restricted stock units vesting		1,538,346		1,538		(1,538	)		-			-			-			-			200,000		200		(200	)		-			-			-			-
Common stock - issued for cash		-		-		-			-			-			-			-
Foreign currency translation adjustments		-		-		-			(28,162	)		-			-			(28,162	)		-		-		-			453,895			-			-			453,895
Net income (loss) for the three months ended March 31, 2019		-		-		-			-			23,896,982			-			23,896,982
Balance at March 31, 2019		94,665,718	$	187,035	$	652,411,876		$	(71,906	)	$	(451,331,581	)	$	(555,188	)	$	200,640,236

	Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals
Balance at December 31, 2019		101,111,797	$	193,481	$	922,050,595		$	(195,550	)	$	(421,964,695	)	$	(555,188	)	$	499,528,643
Stock-based compensation		-		-		12,971,702			-			-			-			12,971,702
Exercise of stock options		214,239		214		1,329,810			-			-			-			1,330,024
Common stock - restricted stock units vesting		422,071		422		(422	)		-			-			-			-
Common stock - issued for cash		-		-		2,235			-			-			-			2,235
Foreign currency translation adjustments		-		-		-			(433,564	)		-			-			(433,564	)
Net income (loss) for the three months ended March 31, 2020		-		-		-			-			(19,835,570	)		-			(19,835,570	)
Balance at March 31, 2020		101,748,107	$	194,117	$	936,353,920		$	(629,114	)	$	(441,800,265	)	$	(555,188	)	$	493,563,470
Net income (loss) for the three months ended June 30, 2020																					-		-		-			-			(13,611,213	)		-			(13,611,213	)
Balance at June 30, 2020																					102,250,872	$	194,620	$	948,532,470		$	(175,219	)	$	(455,411,478	)	$	(555,188	)	$	492,585,205


	Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals			Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals
Balance at September 30, 2018		88,505,302	$	180,875	$	582,902,694		$	(21,564	)	$	(487,265,816	)	$	(555,188	)	$	95,241,001			88,505,302	$	180,875	$	582,902,694		$	(21,564	)	$	(487,265,816	)	$	(555,188	)	$	95,241,001
Stock-based compensation		-		-		5,318,882			-			-			-			5,318,882			-		-		7,276,875			-			-			-			7,276,875
Exercise of stock options		702,242		702		3,674,029			-			-			-			3,674,731			1,244,161		1,244		6,440,761			-			-			-			6,442,005
Common stock - restricted stock units vesting		2,197,305		2,197		(2,197	)		-			-			-			-			2,197,305		2,197		(2,197	)		-			-			-			-
Common stock - issued for cash		3,260,869		3,261		60,518,468			-			-			-			60,521,729			3,260,869		3,261		60,518,468			-			-			-			60,521,729
Foreign currency translation adjustments		-		-		-			(50,342	)		-			-			(50,342	)		-		-		-			(81,514	)		-			-			(81,514	)
Net income (loss) for the six months ended March 31, 2019		-		-		-			-			35,934,235			-			35,934,235
Balance at March 31, 2019		94,665,718	$	187,035	$	652,411,876		$	(71,906	)	$	(451,331,581	)	$	(555,188	)	$	200,640,236
Net income (loss) for the nine months ended June 30, 2019																					-		-		-			-			56,269,944			-			56,269,944
Balance at June 30, 2019																					95,207,637	$	187,577	$	657,136,601		$	(103,078	)	$	(430,995,872	)	$	(555,188	)	$	225,670,040


	Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals			Common Stock		Amount ($)		Additional Paid-In Capital			Accumulated Other Comprehensive Income (Loss)			Accumulated Deficit			Non-controlling Interest			Totals
Balance at September 30, 2019		95,506,271	$	187,876	$	664,086,155		$	(391,624	)	$	(419,290,967	)	$	(555,188	)	$	244,036,252			95,506,271	$	187,876	$	664,086,155		$	(391,624	)	$	(419,290,967	)	$	(555,188	)	$	244,036,252
Stock-based compensation		-		-		17,463,455			-			-			-			17,463,455			-		-		27,509,663			-			-			-			27,509,663
Exercise of stock options		686,432		686		4,330,891			-			-			-			4,331,577			989,197		989		6,463,433			-			-			-			6,464,422
Common stock - restricted stock units vesting		955,404		955		(955	)		-			-			-			-			1,155,404		1,155		(1,155	)		-			-			-			-
Common stock - issued for cash		4,600,000		4,600		250,474,374			-			-			-			250,478,974			4,600,000		4,600		250,474,374			-			-			-			250,478,974
Foreign currency translation adjustments		-		-		-			(237,490	)		-			-			(237,490	)		-		-		-			216,405			-			-			216,405
Net income (loss) for the six months ended March 31, 2020		-		-		-			-			(22,509,298	)		-			(22,509,298	)
Balance at March 31, 2020		101,748,107	$	194,117	$	936,353,920		$	(629,114	)	$	(441,800,265	)	$	(555,188	)	$	493,563,470

Net income (loss) for the nine months ended June 30, 2020																					-		-		-			-			(36,120,511	)		-			(36,120,511	)
Balance at June 30, 2020																					102,250,872	$	194,620	$	948,532,470		$	(175,219	)	$	(455,411,478	)	$	(555,188	)	$	492,585,205

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

	Six Months Ended March 31,						Nine Months Ended June 30,
	2020			2019			2020			2019
CASH FLOWS FROM OPERATING ACTIVITIES:
Net income (loss)	$	(22,509,298	)	$	35,934,235		$	(36,120,511	)	$	56,269,944
Stock-based compensation		17,463,455			5,318,882			27,509,663			7,276,875
Depreciation and amortization		2,631,472			2,353,319			4,167,873			3,356,769
Amortization/(accretion) of note premiums		419,212			330,229			652,747			682,243
Changes in operating assets and liabilities:
Accounts receivable		(604,410	)		(13,094,965	)		(21,031,203	)		(1,716,736	)
Prepaid expenses and other current assets		46,520			(1,440,287	)		(863,287	)		(2,393,230	)
Deferred revenue		(49,630,006	)		120,622,138			(56,530,409	)		97,940,261
Accounts payable		5,767,770			1,256,092			(3,576,053	)		1,824,146
Accrued expenses		(5,424,591	)		(2,340,651	)		(54,217	)		(3,477,235	)
Other		725,481			(240,737	)		1,303,852			(538,020	)
NET CASH PROVIDED BY (USED IN) OPERATING ACTIVITIES		(51,114,395	)		148,698,255			(84,541,545	)		159,225,017
CASH FLOWS FROM INVESTING ACTIVITIES:
Purchases of property and equipment		(7,929,100	)		(946,788	)		(10,067,360	)		(4,170,285	)
Purchases of marketable securities		(180,523,424	)		(90,266,001	)		(193,964,290	)		(90,266,001	)
Proceeds from sale of marketable securities		19,602,967			12,239,219			29,148,287			29,861,219
NET CASH PROVIDED BY (USED IN) INVESTING ACTIVITIES		(168,849,557	)		(78,973,570	)		(174,883,363	)		(64,575,067	)
CASH FLOWS FROM FINANCING ACTIVITIES:
Principal payments on notes payable		-			(2,415,150	)		-			(2,415,150	)
Proceeds from the exercises of stock options		4,331,577			3,674,731			6,464,423			6,442,005
Proceeds from the issuance of common stock		250,478,974			60,521,729			250,478,974			60,521,729
NET CASH PROVIDED BY (USED IN) FINANCING ACTIVITIES		254,810,551			61,781,310			256,943,397			64,548,584
NET INCREASE (DECREASE) IN CASH		34,846,599			131,505,995			(2,481,511	)		159,198,534
CASH AND CASH EQUIVALENTS AT BEGINNING OF PERIOD		221,804,128			30,133,213			221,804,128			30,133,213
CASH AND CASH EQUIVALENTS AT END OF PERIOD	$	256,650,727		$	161,639,208		$	219,322,617		$	189,331,747
Supplementary disclosures:
Interest paid	$	-		$	(27,437	)	$	-		$	(27,437	)
Income Taxes Paid	$	-		$	(2,400	)	$	-		$	(2,400	)

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 collectively to Arrowhead Madison Inc. (“Arrowhead Madison”), Arrowhead Australia Pty Ltd (“Arrowhead Australia”) and Ablaris Therapeutics, Inc. (“Ablaris”), (4) the term “Common Stock” refers to Arrowhead’s Common Stock, (5) the term “Preferred Stock” refers to Arrowhead’s Preferred Stock and (6) the term “Stockholder(s)” refers to the holders of Arrowhead 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, or 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-AAT for liver disease associated with alpha-1 antitrypsin deficiency (AATD), ARO-APOC3 for hypertriglyceridemia, ARO-ANG3 for dyslipidemia, ARO-HSD for liver disease, ARO-ENaC for cystic fibrosis, ARO-HIF2 for renal cell carcinoma, ~~and~~ ARO-LUNG2 as a candidate to treat chronic obstructive pulmonary ~~disease~~disorder (COPD). and ARO-COV for treatment for the current novel coronavirus that causes COVID-19 and other possible future pulmonary-borne pathogens.ARO-JNJ1 is being developed for an undisclosed liver-expressed target under a collaboration agreement with Janssen Pharmaceuticals, Inc. (“Janssen”). ARO-HBV (JNJ-3989) for chronic hepatitis B virus was out-licensed to Janssen in October 2018. ARO-LPA (AMG 890)for cardiovascular disease was out-licensed to Amgen Inc. (“Amgen”) in 2016.

Arrowhead operates a lab facility in Madison, Wisconsin, where the Company’s research and development activities, including the development of RNAi therapeutics, are based. The Company’s principal executive offices are located in Pasadena, California. ~~During the three months ended~~In March ~~31,~~ 2020, the Company entered into a sublease for additional research and development facility space in San Diego, California as discussed further in Note 8 below.

During ~~the first half of~~ fiscal year 2020, the Company has continued to develop its pipeline and partnered candidates. The Company has began dosing in an adaptive design phase 2/3 trial, called SEQUOIA, with the potential to serve as a pivotal registration study of ARO-AAT. The Company also began dosing in its ARO-AAT 2002 study, a pilot open-label, multi-dose Phase 2 study to assess changes in novel histological activity scale in response to ARO-AAT over time in patients with alpha-1 antitrypsin deficiency associated liver disease. In addition, the Company also dosed the first patients in AROHSD1001, a Phase 1/2 clinical study of ARO-HSD, the Company’s investigational RNA interference therapeutic being developed as a treatment for patients with alcohol related and nonalcohol related liver diseases, such as nonalcoholic steatohepatitis (NASH). The Company also presented new clinical data on its two cardiometabolic candidates, ARO-APOC3 and ARO-ANG3, in two late-breaking oral presentations at the American Heart Association Scientific Sessions 2019. ~~The~~In addition, the Company ~~also~~ filed an ~~IND~~investigational new drug (“IND”) application to begin a phase 1b study of ARO-HIF2 ~~filed a CTA to begin a phase 1 study of ARO-HSD,~~ and filed a ~~CTA~~clinical trials application (“CTA”) to begin a phase 1 study of ARO-ENaC.

The Company’s partnered candidates under its collaboration agreements with Janssen and Amgen also continue 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, and in connection with the start of this study Arrowhead earned a $25 million milestone payment under the License Agreement (“Janssen License Agreement”). Janssen has also nominated the first of 3 potential candidates under the Research Collaboration and Option Agreement (“Janssen Collaboration Agreement”), ARO-JNJ1, and the Company is currently performing discovery, optimization and preclinical research and development for this candidate. Under the terms of the Janssen agreements taken together, the Company has received $175 million as an upfront payment, $75 million in the form of an equity investment by JJDC in Arrowhead common stock, two $25 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 up to mid teens under the Janssen License Agreement and up to low teens under the Janssen Collaboration Agreement on product sales. The Company’s collaboration agreement with Amgen for AMG 890 (ARO-LPA), (the “Second Collaboration and License Agreement” or “AMG 890 (ARO-LPA) Agreement”), continues to progress. The Company has received $35 million in upfront payments, $21.5 million in the form of an equity investment by Amgen in the Company’s Common Stock, a $10 million milestone payment, and may receive up to $420 million in development, regulatory and sales milestone payments. The Company is eligible to receive up to low double-digit royalties for sales of products under the AMG 890 (ARO-LPA) Agreement. In July 2020, Amgen initiated a Phase 2 clinical study, which will result in a $20 million milestone payment to the Company.

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

The Company is actively monitoring the ~~novel coronavirus (“COVID-19”) situation.~~ongoing COVID-19 pandemic. The financial results for the three and ~~six~~nine months ended ~~March 31,~~June 30, 2020 were not significantly impacted by COVID-19. The Company ~~has~~temporarily paused enrollment in its two ARO-AAT ~~studies:~~studies, SEQUOIA and the ARO-AAT 2002 study, but ~~now is working with sites and investigators to begin~~resumed the process of ~~resuming~~ screening and ~~enrollment. Patients~~enrolling patients during the three months ended June 30, 2020. During the pause in enrollment, patients already enrolled in these studies ~~continue~~continued to be dosed per protocol and ~~continue~~continued to come in for their follow up visits. Additional delays have occurred in the Company’s earlier stage programs, but we do not expect a material impact to any program’s anticipated timelines. Several of the Company’s other clinical candidates are in the start-up stage (ARO-HSD, ARO-HIF2 and ARO-ENaC), during which significant clinical costs will continue to be incurred. Additionally, the Company’s operations at its research and development ~~facility~~facilities in Madison, WIWisconsin and San Diego, California, and its corporate headquarters in Pasadena, CACalifornia have continued to operate with limited impact, other than for enhanced safety measures, including work from home policies. However, the Company cannot predict the impact of the progression of COVID-19 will have on future financial 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 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, which contemplate the continuation of the Company as a going concern. Historically, the Company’s primary source of financing has been through the sale of its securities. Research and development activities have required significant capital investment since the Company’s inception. The Company expects its operations to continue to require cash investment to pursue its research and development goals, including clinical trials and related drug manufacturing.

At ~~March 31,~~June 30, 2020 the Company had ~~$256.7~~$219.3 million in cash and cash equivalents (including $1.8 million in restricted cash), ~~$51.0~~$67.7 million in short-term investments, and ~~$190.6~~$177.5 million in long-term investments to fund operations. During the ~~six~~nine months ended ~~March 31,~~June 30, 2020, the Company’s cash and investments balance increased by $~~195.4~~$161.7 million, which was primarily the result of the December 2019 securities offering that generated $250.5 million in net cash proceeds for the Company, as discussed further in Note 6 below. These cash inflows were partially offset by cash outflows primarily related to operating activities.

There have been no changes to the significant accounting policies disclosed in the Company’s most recent Annual Report on Form 10-K, except as a result of the Financial Accounting Standards ~~Board (FASB)’s~~Board’s (“FASB”) Accounting Standards Update ~~(ASU)~~(“ASU”) No. 2016-02, Leases (ASC 842), as discussed below.

Leases — The Company determines whether a contract is, or contains, a lease at inception. The Company classifies each of its leases as operating or financing considering factors such as the length of the lease term, the present value of the lease payments, the nature of the asset being leased, and the potential for ownership of the asset to transfer during the lease term. Leases with terms greater than one-year are recognized on the Consolidated Balance Sheets as Right-of-use assets and Lease liabilities and are measured at the present value of the fixed payments due over the expected lease term less the present value of any incentives, rebates or abatements expected to be received from the lessor. Options to extend a lease are typically excluded from the expected lease term as the exercise of the option is typically not reasonably certain. The interest rate implicit in lease contracts is typically not readily determinable. As such, the Company utilizes the appropriate incremental borrowing rate, which is the rate incurred to borrow on a collateralized basis an amount equal to the lease payments over a similar term and in a similar economic environment. The Company records expense to recognize fixed lease payments on a straight-line basis over the expected lease term. Costs determined to be variable and not based on an index or rate are not included in the measurement of the lease liability and are expensed as incurred.

In March 2016, the FASB issued ASU No. 2016-02, Leases (Topic ASC 842). Under ASC 842, lessees are required to recognize a right-of-use asset and a right-of-use lease liability for virtually all leases other than those that meet the definition of a short-term lease. For income statement purposes, a dual model was retained, requiring leases to be classified as either operating or finance. Operating leases will result in straight-line expense while finance leases will result in a front-loaded expense pattern (similar to current capital leases). The Company adopted this standard effective October 1, 2019 and elected the package of three practical expedients that permits an entity to a) not reassess whether expired or existing contracts contain leases, b) not reassess lease classification for existing or expired leases, and c) not consider whether previously capitalized initial direct costs would be appropriate under the new standard. At ~~March 31,~~June 30 2020, the Company has recorded right-of-use assets of ~~$10.3~~$16.5 million and right-of-use liabilities of ~~$14.9~~

$21.4 million on its Consolidated Balance Sheets for its research and development facility ~~lease~~leases in Madison, Wisconsin and San Diego, California, as well as its corporate headquarters lease in Pasadena, California, as discussed further in Note 8 below. The adoption of this standard did not have a material impact on the Company’s Consolidated Statement of Comprehensive Income (Loss) and the Company’s Consolidated Statement of Cash Flows.

In November 2018, the FASB issued ASU No. 2018-18 Collaborative Arrangements (Topic 808). This update provides clarification 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 becomes effective for the Company in the first quarter of fiscal 2021 with early adoption permitted. The Company does not expect the adoption of this update to have a material effect on its Consolidated Financial Statements.

On September 28, 2016, the Company entered into 2 Collaboration and License agreements, and a Common Stock Purchase Agreement with Amgen Inc., a Delaware corporation (“Amgen”). Under one of the license agreements (the “Second Collaboration and License Agreement” or “AMG 890 (ARO-LPA) Agreement”), Amgen has received a worldwide, exclusive license to Arrowhead’s novel, RNAi 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 license agreement (the “First Collaboration and License Agreement” or “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. In both agreements, Amgen is wholly responsible for clinical development and commercialization. Under the terms of the agreements taken together, the Company has received $35 million in upfront payments, $21.5 million in the form of an equity investment by Amgen in the Company’s Common Stock, and a $10 million milestone payment, and may receive up to $420 million in 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 AMG 890 (ARO-LPA) 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 substantially completed its performance obligations under the AMG 890 (ARO-LPA) 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, which will result in a $20 million milestone payment to the Company. During the three ~~and six~~ months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized $20.0 million and $0 million of Revenue associated with its agreements with Amgen, respectively. During the nine months ended June 30, 2020 and 2019, the Company recognized $20.0 million and $0.3 million of Revenue associated with its agreements with Amgen, respectively. As of ~~March 31,~~June 30, 2020, there were $0$20.0 million in contract assets recorded as accounts receivable, and $0 contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets.

On October 3, 2018, the Company entered into a License Agreement (“Janssen License Agreement”) and a Research Collaboration and Option Agreement (“Janssen Collaboration Agreement”) with Janssen Pharmaceuticals, Inc. (“Janssen”) part of the Janssen Pharmaceutical Companies of Johnson & Johnson. The Company also entered into a Stock Purchase Agreement (“JJDC Stock Purchase Agreement”) with Johnson & Johnson Innovation-JJDC, Inc. (“JJDC”), a New Jersey corporation. 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 potentially curative therapy for patients with chronic hepatitis B virus infection. Beyond the Company’s ongoing Phase ~~1 /~~ 1/2 study of JNJ-3989 (ARO-HBV), Janssen will be wholly responsible for clinical development and commercialization. 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 will not include candidates in the Company’s current pipeline. The Company will perform discovery, optimization and preclinical research and development, entirely funded by Janssen, 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 million as an upfront payment, $75 million in the form of an equity investment by JJDC in Arrowhead common stock under the JJDC Stock Purchase Agreement, and two $25 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 up to mid teens under the Janssen License Agreement and up to low teens under the Janssen Collaboration Agreement on product sales.

The Company has evaluated these agreements in accordance with the new revenue recognition standard that became effective for the Company on October 1, 2018. The adoption of the new revenue standard did not have a material impact on the balances reported when evaluated under the superseded revenue standard. At the inception of these agreements, the Company has 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 ongoing Phase ~~1 /~~ 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 will be accounted for if and when it is exercised.

The Company determined the transaction price totaled approximately ~~$252.5~~$252.6 million which includes the upfront payment, the premium paid by JJDC for its equity investment in the Company, the two $25 million milestone payments earned and estimated payments for reimbursable Janssen R&D services to be performed. The Company has allocated the total ~~$252.5~~$252.6 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 will be recognized using a proportional performance method (based on actual labor hours versus estimated total labor hours) beginning in October 2018 and ending as the Company’s efforts in overseeing the ongoing phase ~~1 /~~ 1/2 clinical trial are completed. During the three months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized approximately ~~$22.2~~$6.9 million and ~~$47.9~~$42.3 million of Revenue associated with its agreements with Janssen and JJDC, respectively. During the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized approximately ~~$50.9~~$57.9 million and ~~$82.5~~$124.8 million of Revenue associated with its agreements with Janssen and JJDC, respectively. As of ~~March 31,~~June 30, 2020, there were $0 in contract assets recorded as accounts receivable, and ~~$33.2~~$26.3 million of contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets. The ~~$33.2~~$26.3 million of current deferred revenue is driven by the upfront payment, the premium paid by JJDC for its equity investment in the Company, and the two $25 million milestone payments earned, net of revenue recognized to date.

Janssen has also selected the first of the three targets under the Janssen Collaboration Agreement, now referred to as ARO-JNJ1, and the Company has begun to conduct its discovery, optimization and preclinical research and development of ARO-JNJ1. All costs and labor hours spent by the Company will be entirely funded by Janssen. During the three months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized approximately ~~$1.4~~$0.4 million and $0$0.4 million of Revenue associated with its efforts on the ARO-JNJ1 candidate, respectively. During the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized ~~$2.1~~$2.4 million and $0$0.4 million of Revenue associated with these efforts on the ARO-JNJ1 candidate, respectively. As of ~~March 31,~~June 30, 2020, there were ~~$1.3~~$1.7 million of contract assets recorded as accounts receivable, and $0 of contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets.

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

	March 31, 2020			September 30, 2019			June 30, 2020			September 30, 2019
Computers, office equipment and furniture	$	635,769		$	637,577		$	661,927		$	637,577
Research equipment		18,098,960			12,932,304			19,514,871			12,932,304
Software		293,189			147,254			293,189			147,254
Leasehold improvements		24,187,465			21,579,415			24,883,656			21,579,415
Total gross fixed assets		43,215,383			35,296,550			45,353,643			35,296,550
Less: Accumulated depreciation and amortization		(13,852,642	)		(12,081,651	)		(14,963,936	)		(12,081,651	)
Property and equipment, net	$	29,362,741		$	23,214,899		$	30,389,707		$	23,214,899

Depreciation and amortization expense for property and equipment for the three months ended ~~March 31,~~June 30, 2020 and 2019 was ~~$946,481~~$1,111,293 and ~~$750,860,~~$578,342, respectively. Depreciation and amortization expense for property and equipment for the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019 was ~~$1,781,258~~$2,892,551 and ~~$1,503,105,~~$2,081,447, respectively.

The Company invests a portion of its excess cash balances in short-term and long-term debt securities. Investments at ~~March 31,~~June 30, 2020 consisted of corporate bonds with maturities remaining of less than ~~or equal to~~ 36 months. 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 investments in accordance with FASB ASC 320, Investments – Debt and Equity Securities. At ~~March 31,~~June 30, 2020, all investments were classified as held-to-maturity securities.

The following tables summarize the Company’s short-term and long-term investments as of ~~March 31,~~June 30, 2020 and September 30, 2019.

	As of March 31, 2020								As of June 30, 2020
	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)	$	50,959,058	$	264,194	$	(37,786)	$	51,185,466	$	67,709,263	$	1,188,416	$	—	$	68,897,679
Commercial notes (due within one through three years)	$	190,618,075	$	1,735,812	$	(1,481,115)	$	190,872,772	$	177,529,881	$	5,845,177	$	(14,833)	$	183,360,225
Total	$	241,577,133	$	2,000,006	$	(1,518,901)	$	242,058,238‬	$	245,239,144	$	7,033,593	$	(14,833)	$	252,257,904‬

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 ~~approximately $754,394.~~$791,495. 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 ~~approximately $7,889,455.~~$8,277,460. Amortization expense for the three months ended ~~March 31,~~June 30, 2020 and 2019 was $425,107 and ~~$425,108,~~$425,107, respectively. Amortization expense for the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019 was ~~$850,214~~$1,275,322 and ~~$850,215,~~$1,275,322, respectively. Amortization expense is expected to be ~~$850,215~~$425,107 for the remainder of fiscal 2020, $1,700,429 in 2021, $1,700,429 in 2022, $1,700,429 in 2023, $1,700,429 in 2024, and $8,561,435 thereafter.

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

	Intangible assets subject to amortization			Intangible assets subject to amortization
Balance at September 30, 2019	$	17,063,580		$	17,063,580
Impairment		—			—
Amortization		(850,214	)		(1,275,322	)
Balance at March 31, 2020	$	16,213,366
Balance at June 30, 2020				$	15,788,258

At ~~March 31,~~June 30, 2020, 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 31,~~June 30, 2020, ~~101,748,107~~102,250,872 shares of Common Stock were outstanding. At ~~March 31,~~June 30, 2020, ~~8,474,561~~8,252,796 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 and 2013 Incentive Plan, as well as for inducement grants made to new employees.

In December ~~31,~~ 2019, the Company sold 4,600,000 shares of its Common Stock in a public offering at a price of $58.00 per share. The aggregate purchase price paid by the investors for the Common Stock was $266.8 million, and the Company received net proceeds of $250.5 million after deducting advisory fees and offering expenses.

Effective August 5, 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 (“ATM 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. No sales have been made under the ATM Agreement.

On occasion, 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 ~~March 31,~~June 30, 2020.

In the normal course of business, the Company enters into various purchase commitments for the manufacture of drug components, for toxicology studies, and for clinical studies. As of ~~March 31,~~June 30, 2020, these future commitments were estimated at approximately ~~$72.2~~$83.0 million, of which approximately ~~$40.0~~$20.5 million is expected to be incurred in fiscal 2020, and ~~$32.2~~$62.5 million is expected to be incurred beyond fiscal 2020.

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 NDA 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 31,~~June 30, 2020, the Company did 0t accrue any milestone payment. During the nine months ended June 30, 2020, the Company accrued a $0.9 million milestone payment related to the progression of the ARO-ENaC program. During the three and ~~six~~nine months ended ~~March 31,~~June 30, 2019, the Company did 0t accrue for any milestone payments. In 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 ~~new~~ 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, and this lease has replaced the Company’s previous corporate headquarters office lease.~~California. The increased capacity of this new office space compared to the Company’s ~~current~~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 ~~$8.8~~$8.7 million over the term. The lease expires on April 30, 2027. The Company ~~expects to pay~~has paid approximately $3.5 million for leasehold improvements, net of tenant improvement allowances. The lease contains an option to renew for 1 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 31,~~June 30, 2020.

In January 2016, the Company ~~also leases approximately 74,000 square feet of office and laboratory space~~entered into a lease for its research facility in Madison, Wisconsin. The lease ~~will expire~~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 to expand the rentable square feet by an additional 14,000 square feet and to extend the lease expiration date to September 2029. In May 2020, the Company further amended the lease to increase the rentable square feet by an additional 26,000 square feet and extended the lease expiration date to September 30, 2031. Lease payments are estimated to total approximately ~~$13.3~~$26.2 million for the term. The lease contains 2 options to renew for two 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 31,~~June 30, 2020.

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 lease 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. Lease payments are estimated to total approximately $2.0 million over the term.

Operating lease cost during the three and ~~six~~nine months ended ~~March 31,~~June 30, 2020 was ~~$0.5~~$0.8 million and ~~$0.9~~$1.7 million, respectively. Variable lease costs during the three and ~~six~~nine months ended ~~March 31,~~June 30, 2020 were $0.2 million and ~~$0.3~~$0.6 million, respectively. There was 0 short-term lease cost during the three and ~~six~~nine months ended ~~March 31,~~June 30, 2020.

The following table presents maturities of operating lease liabilities on an undiscounted basis as of ~~March 31,~~June 30, 2020:

2020 (remainder of fiscal year)	$	936,566	$	681,214
2021		2,256,379		3,091,900
2022		2,521,446		3,853,290
2023		2,590,558		3,406,754
2024		2,661,512		3,269,674
2025 and thereafter		10,834,206		18,689,588
Total lease payments		21,800,667		32,992,420
Less imputed interest		(6,933,478)		(11,620,743)
Total operating lease liabilities (includes current portion)	$	14,867,189	$	21,371,677

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 of Cash Flow for the three and ~~six~~nine months ended ~~March 31,~~June 30, 2020 was ~~$0.3~~$0.5 million and ~~$0.6~~$1.1 million, respectively. The weighted-average remaining lease term and weighted-average discount rate for all leases as of ~~March 31,~~June 30, 2020 was ~~8.6~~9.6 years and ~~8.9%~~8.4%, respectively.

As of September 30, 2019, future minimum lease payments due in fiscal years under operating leases were as follows:

During the three months ended March 31, 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 space consists of approximately 21,000 rentable square feet located at 11404 Sorento Valley Road, San Diego, California, 92121. The term of the Sublease commenced on April 1, 2020 and will expire on January 14, 2023. Lease payments are estimated to total approximately $2.1 million over the term.

Arrowhead has two plans that provide for equity-based compensation. Under the 2004 Equity Incentive Plan and 2013 Incentive Plan, as of ~~March 31,~~June 30, 2020, ~~886,598~~744,250 and ~~5,972,038~~5,652,008 shares, respectively, of Arrowhead’s Common Stock are reserved for the grant of stock options, stock appreciation rights, restricted stock awards and performance unit/share awards to employees, consultants and others. No further grants may be made under the 2004 Equity Incentive Plan. As of ~~March 31,~~June 30, 2020, there were options granted and outstanding to purchase ~~886,598~~744,250 and ~~2,798,538~~2,672,851 shares of Common Stock under the 2004 Equity Incentive Plan and the 2013 Incentive Plan, respectively, and there were ~~2,783,000~~2,583,000 restricted stock units granted and outstanding under the 2013 Incentive Plan. Also, as of ~~March 31,~~June 30, 2020, there were ~~1,024,850~~1,112,463 shares reserved for options and ~~591,075~~744,075 shares reserved for restricted stock units issued as inducement grants to new employees outside of equity compensation plans. During the three months ended ~~March 31,~~June 30, 2020, ~~306,500~~0 options and ~~1,744,071~~0 restricted stock units were granted under the 2013 Incentive Plan, and ~~126,000~~134,000 options and ~~300,000~~153,000 restricted stock units were granted as inducement awards to new employees outside of equity incentive plans. During the ~~six~~nine months ended ~~March 31,~~June 30, 2020, 310,500 options and 1,749,071 restricted stock units were granted under the 2013 Incentive Plan, and ~~343,000~~477,000 options and ~~584,575~~737,575 restricted stock units were granted as inducement awards to new employees outside of the equity incentive plans.

	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, 2019		4,773,670		$	8.16					4,773,670		$	8.16
Granted		653,500		53.78						787,500		50.42
Cancelled		(30,752	)	15.00						(42,409	)	25.04
Exercised		(686,432	)	6.31						(989,197	)	6.54
Balance At March 31, 2020		4,709,986		$	14.72	6.2 years	$	82,658,407
Exercisable At March 31, 2020		3,111,009		$	7.12	4.8 years	$	67,796,517
Balance At June 30, 2020										4,529,564		$	15.71	6.2 years	$	133,654,814
Exercisable At June 30, 2020										2,928,765		$	7.66	4.8 years	$	104,700,213

Stock-based compensation expense related to stock options for the three months ended ~~March 31,~~June 30, 2020 and 2019 was ~~$2,527,839~~$2,659,265 and ~~$1,017,065,~~$1,016,206, respectively. Stock-based compensation expense related to stock options for the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019 was ~~$4,136,910~~$6,796,175 and ~~$1,807,500,~~$2,823,706, 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 31,~~June 30, 2020 and 2019 was ~~$17,968,884~~$3,421,181 and ~~$7,580,360,~~$1,316,220, respectively. The grant date fair value of the options granted by the Company for the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019 was ~~$26,599,374~~$30,020,524 and ~~$8,137,249,~~$9,453,469, respectively.

The intrinsic value of the options exercised during the three months ended ~~March 31,~~June 30, 2020 and 2019 was ~~$8,605,235~~$9,529,237 and ~~$6,806,594,~~$9,349,226, respectively. The intrinsic value of the options exercised during the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019 was ~~$30,245,825~~$39,775,062 and ~~$8,122,294,~~$17,471,520, respectively.

As of ~~March 31,~~June 30, 2020, the pre-tax compensation expense for all outstanding unvested stock options in the amount of ~~$34,707,355~~$35,021,715 will be recognized in the Company’s results of operations over a weighted average period of ~~3.5~~3.3 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,		Nine Months Ended June 30,
	2020	2019	2020	2019
Dividend yield	—	—	—	—
Risk-free interest rate	0.5 – 1.8%	2.3 – 3.1%	0.4 – 1.8%	1.9 – 3.1%
Volatility	90.5 – 91.8%	115%	90.5 – 91.9%	115%
Expected life (in years)	6.25	6.25	6.25	6.25
Weighted average grant date fair value per share of options granted	$40.70	$11.42	$38.12	$12.21

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

Restricted stock units (RSUs), including time-based and performance-based awards, were granted under the Company’s 2013 Incentive Plan and as inducements grants granted outside of the Plan. During the three months ended ~~March 31,~~June 30, 2020, the Company issued ~~1,744,071~~0 RSUs under the 2013 Incentive Plan and ~~300,000~~153,000 RSUs as inducement awards. During the ~~six~~nine months ended ~~March 31,~~June 30, 2020, the Company issued 1,749,071 RSUs under the 2013 Incentive Plan and ~~584,575~~737,575 RSUs as inducement awards. At vesting, each outstanding RSU will be exchanged for one share of the Company’s Common Stock. RSU recipients may elect to net share settle upon vesting, in which case the Company pays the employee’s income taxes due upon vesting and withholds a number of shares of Common Stock of equal value. 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, 2019		2,062,833		$	9.43		2,062,833		$	9.43
Granted		2,333,646			58.27		2,486,646			57.04
Vested		(955,404	)		9.07		(1,155,404	)		9.65
Forfeited		(67,000	)		31.78		(67,000	)		31.78
Unvested at March 31, 2020		3,374,075		$	42.87
Unvested at June 30, 2020							3,327,075		$	44.49

During the three months ended ~~March 31,~~June 30, 2020 and 2019, the Company recorded ~~$10,443,863~~$7,386,943 and ~~$1,584,283~~$941,788 of expense related to RSUs, respectively. During the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019, the Company recorded ~~$13,326,545~~$20,713,488 and ~~$3,511,381~~$4,453,169 of expense related to RSUs, respectively. Such expense is included in stock-based compensation expense in the Company’s Consolidated Statement 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.

As of ~~March 31,~~June 30, 2020 the pre-tax compensation expense for all unvested RSUs in the amount of ~~$89,156,048~~$87,634,315 will be recognized in the Company’s results of operations over a weighted average period of ~~3.5~~3.3 years.

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 31,~~June 30, 2020 and September 30, 2019 for assets and liabilities measured at fair value on a recurring basis:

	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Cash and cash equivalents	$	256,650,727	$	—	$	—	$	256,650,727	$	219,322,617	$	—	$	—	$	219,322,617
Short-term investments	$	51,185,466	$	—	$	—	$	51,185,466	$	68,897,679	$	—	$	—	$	68,897,679
Long-term investments	$	190,872,772	$	—	$	—	$	190,872,772	$	183,360,225	$	—	$	—	$	183,360,225
Contingent consideration	$	—	$	—	$	—	$	—	$	—	$	—	$	—	$	—

The Company had a liability for contingent consideration related to its acquisition of the Roche RNAi business completed in 2011. The fair value measurement of the contingent consideration obligations is determined using Level 3 inputs. The fair value of contingent consideration obligations is based on a discounted cash flow model using a probability-weighted income approach. The measurement is based upon unobservable inputs supported by little or no market activity based on the Company’s assumptions and experience. Estimating timing to complete the development and obtain approval of products is difficult, and there are inherent uncertainties in developing a product candidate, such as obtaining FDA and other regulatory approvals. In determining the probability of regulatory approval and commercial success, the Company utilizes data regarding similar milestone events from several sources, including industry studies and its own experience. These fair value measurements represent Level 3 measurements as they are based on significant inputs not observable in the market. Significant judgment is employed in determining the appropriateness of these assumptions as of the acquisition date and for each subsequent period. Accordingly, changes in assumptions could have a material impact on the amount of contingent consideration expense the Company records in any given period. In November 2016, the Company announced the discontinuation of its clinical trial efforts for ARC-520, ARC-AAT and ARC-521. Given this development, the Company assessed the fair value of its contingent consideration obligation to be $0 at ~~March 31,~~June 30, 2020 and September 30, 2019.

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,” “could,” “estimate,” or “continue” or the negative 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, 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. As such, our actual results may differ significantly 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 described in other documents we file from time to time with the Securities and Exchange Commission (“SEC”), including subsequent quarterly reports on Form 10-Q. 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, or 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~~Company's pipeline includes ARO-AAT for liver disease associated with alpha-1 antitrypsin deficiency (AATD), ARO-APOC3 for hypertriglyceridemia, ARO-ANG3 for dyslipidemia, ARO-HSD for liver disease, ARO-ENaC for cystic fibrosis, ARO-HIF2 for renal cell carcinoma, ~~and~~ ARO-LUNG2 as a candidate to treat chronic obstructive pulmonary ~~disease~~disorder (COPD). and ARO-COV for treatment for the current novel coronavirus that causes COVID-19 and other possible future pulmonary-borne pathogens.ARO-JNJ1 is being developed for an undisclosed liver-expressed target under a collaboration agreement with Janssen Pharmaceuticals, Inc. (“Janssen”). ARO-HBV (JNJ-3989) for chronic hepatitis B virus was out-licensed to Janssen in October 2018. ARO-LPA (AMG 890)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 of~~ fiscal year 2020, the Company has continued to develop its pipeline and partnered candidates. The Company has began dosing in an adaptive design phase 2/3 trial, called SEQUOIA, with the potential to serve as a pivotal registration study of ARO-AAT. The Company also began dosing in its ARO-AAT 2002 study, a pilot open-label, multi-dose Phase 2 study to assess changes in novel histological activity scale in response to ARO-AAT over time in patients with alpha-1 antitrypsin deficiency associated liver disease. In addition, the Company also dosed the first patients in AROHSD1001, a Phase 1/2 clinical study of ARO-HSD, the Company’s investigational RNA interference therapeutic being developed as a treatment for patients with alcohol related and nonalcohol related liver diseases, such as nonalcoholic steatohepatitis (NASH). The Company also presented new clinical data on its two cardiometabolic candidates, ARO-APOC3 and ARO-ANG3, in two late-breaking oral presentations at the American Heart Association Scientific Sessions 2019. ~~The~~In addition, the Company ~~also~~ filed an ~~IND~~investigational new drug (“IND”) application to begin a phase 1b study of ARO-HIF2 and filed a ~~CTA~~clinical trials application (“CTA”) to begin a phase 1 study of ~~ARO-HSD, and filed a CTA to begin phase 1 study of~~ ARO-ENaC.

The Company’s partnered candidates under its collaboration agreements with Janssen and Amgen also continue 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, and in connection with the start of this study Arrowhead earned a $25 million milestone payment under the License Agreement (“Janssen License Agreement”). Janssen has also nominated the first of 3 potential candidates under the Research Collaboration and Option Agreement (“Janssen Collaboration Agreement”), ARO-JNJ1, and the Company is currently performing discovery, optimization and preclinical research and development for this candidate. Under the terms of the Janssen agreements taken together, the Company has received $175 million as an upfront payment, $75 million in the form of an equity investment by Johnson & Johnson Innovation-JJDC, Inc. (“JJDC”) in Arrowhead common stock under the Stock Purchase Agreement (“JJDC Stock Purchase Agreement”), two $25 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 three additional targets covered under the Janssen Collaboration Agreement. The Company is further eligible to receive tiered royalties up to mid teens under the Janssen License Agreement and up to low teens under the Janssen Collaboration Agreement on product sales. The Company’s collaboration agreement with Amgen for AMG 890 (ARO-LPA), (the “Second Collaboration and License Agreement” or “AMG 890 (ARO-LPA) Agreement”), continues to progress. The Company has received $35 million in upfront payments, $21.5 million in the form of an equity investment by Amgen in the Company’s Common Stock, a $10 million milestone payment, and may receive up to $420 million in development, regulatory and sales milestone payments. The Company is eligible to receive up to low double-digit royalties for sales of products under the AMG 890 (ARO-LPA) Agreement. In July 2020, Amgen initiated a Phase 2 clinical study, which will result in a $20 million milestone payment to the Company.

The Company continues to develop other clinical candidates for future clinical trials. Clinical candidates are tested internally and through GLP toxicology studies at outside laboratories. Drug materials for such studies and clinical trials are either contracted to third-party manufactures or manufactured internally. The Company engages third-party contract research organizations (CROs) to manage clinical trials and works cooperatively with such organizations on all aspects of clinical trial management, including plan design, patient recruiting, and follow up. These outside costs, relating to the preparation for and administration of clinical trials, are referred to as “program costs”. If the clinical candidates progress through human testing, program costs will increase.

The Company is actively monitoring the ~~novel coronavirus (“COVID-19”) situation.~~COVID-19 pandemic. The financial results for the three and ~~six~~nine months ended ~~March 31,~~June 30, 2020 were not significantly impacted by COVID-19. The Company ~~has~~temporarily paused enrollment in its two ARO-AAT ~~studies:~~studies, SEQUOIA and the ARO-AAT 2002 study, but ~~now is working with sites and investigators to begin~~resumed the process of ~~resuming~~ screening and ~~enrollment. Patients~~enrolling patients during the three months ended June 30, 2020. During the pause in enrollment, patients already enrolled in these studies ~~continue~~continued to be dosed per protocol and ~~continue~~continued to come in for their follow up visits. Additional delays have occurred in the Company’s earlier stage programs, but we do not expect a material impact to any program’s anticipated timelines. Several of the Company’s other clinical candidates are in the start-up stage (ARO-HSD, ARO-HIF2 and ARO-ENaC), during which significant clinical costs will continue to be incurred. Additionally, the Company’s operations at its research and development ~~facility~~facilities in Madison, WIWisconsin and San Diego, California, as well as its corporate headquarters in Pasadena, CACalifornia have continued to operate with limited impact, other than for enhanced safety measures, including work from home policies. However, the Company cannot predict the impact of the progression of COVID-19 will have on future financial 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 of the COVID-19 pandemic.

Net losses were ~~$19.8~~$13.6 million for the three months ended ~~March 31,~~June 30, 2020 as compared to net income of ~~$23.9~~$20.3 million for the three months ended ~~March 31,~~June 30, 2019. Net losses were ~~$22.5~~$36.1 million for the ~~six~~nine months ended ~~March 31,~~June 30, 2020 as compared to net income of ~~$35.9~~$56.3 million for the ~~six~~nine months ended ~~March 31,~~June 30, 2019. Net losses per share – diluted were ~~$0.20~~$0.13 for the three months ended ~~March 31,~~June 30, 2020 as compared to net income per share - diluted of ~~$0.24~~$0.21 for the three months ended ~~March 31,~~June 30, 2019. Net losses per share – diluted were ~~$0.23~~$0.36 for the ~~six~~nine months ended ~~March 31,~~June 30, 2020 as compared to net income per share – diluted of ~~$0.37~~$0.58 for the ~~six~~nine months ended ~~March 31,~~June 30, 2019. An increase in research and development and general and administrative expenses coupled with a decrease in revenue from the license and collaboration agreements with Janssen were the drivers of the increase in net losses and net losses per share, as discussed further below.

The Company strengthened its liquidity and financial position through the Janssen License Agreement, Janssen Collaboration Agreement and JJDC Stock Purchase Agreement, executed in October 2018. Under the terms of the agreements taken together, the Company has received $175 million as an upfront payment, $75 million in the form of an equity investment by JJDC in Arrowhead common stock, and two $25 million milestone payments. Additionally, in December 2019, the Company completed a securities offering which generated approximately $250.5 million in net cash proceeds. Moreover, effective August 5, 2020, the Company entered into an Open Market Sale Agreement with Jefferies LLC (the “ATM Agreement”), which provides that, subject to the conditions and limitations set forth in the ATM Agreement, the Company may elect, from time to time, to issue and sell shares of the Company’s common stock up to $250 million. These cash proceeds secure the funding needed to continue to advance our pipeline candidates. The Company had ~~$256.7~~$219.3 million of cash and cash equivalents, ~~$51.0~~$67.7 million in short-term investments, ~~$190.6~~$177.5 million of long term investments and ~~$561.1~~$555.7 million of total assets as of ~~March 31,~~June 30, 2020, as compared to $221.8 million, $36.9 million, $44.2 million and $349.8 million as of September 30, 2019, respectively. 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.

Management makes certain judgments and uses certain estimates and assumptions when applying ~~GAAP~~generally accepted accounting principles in the United States (“GAAP”) in the preparation of our Consolidated Financial Statements. We evaluate our estimates and judgments on an ongoing basis and base our estimates on historical experience and on assumptions that we believe to be reasonable under the circumstances. Our experience and assumptions form the basis for our judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may vary from what we anticipate and different assumptions or estimates about the future could change our reported results. We believe the following accounting policies are the most critical to us, in that they require our most difficult, subjective or complex judgments in the preparation of our consolidated financial statements. For further information, see Note 1, Organization and Significant Accounting Policies, to our Consolidated Financial Statements, which outlines our application of significant accounting policies.

Leases - The Company determines whether a contract is, or contains, a lease at inception. The Company classifies each of its leases as operating or financing considering factors such as the length of the lease term, the present value of the lease payments, the nature of the asset being leased, and the potential for ownership of the asset to transfer during the lease term. Leases with terms greater than one-year are recognized on the Consolidated Balance Sheets as Right-of-use assets and Lease liabilities and are measured at the present value of the fixed payments due over the expected lease term minus the present value of any incentives, rebates or abatements expected to be received from the lessor. Options to extend a lease are typically excluded from the expected lease term as the exercise of the option is typically not reasonably certain. The interest rate implicit in lease contracts is typically not readily determinable. As such, the Company utilizes the appropriate incremental borrowing rate, which is the rate incurred to borrow on a collateralized basis an amount equal to the lease payments over a similar term and in a similar economic environment. The Company records expense to recognize fixed lease payments on a straight-line basis over the expected lease term. Costs determined to be variable and not based on an index or rate are not included in the measurement of the lease liability and are expensed as incurred.

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

	Three Months Ended		Three Months Ended		Three Months Ended		Three Months Ended
	March 31, 2020		March 31, 2019		June 30, 2020		June 30, 2019
Revenue	$	23,528,853	$	48,148,275	$	27,375,778	$	42,696,636
Operating Income (Loss)		(22,240,255)		22,010,692		(15,945,862)		18,595,749
Net Income (Loss)		(19,835,570)		23,896,982		(13,611,213)		20,335,708
Net Income (Loss) per Share (Diluted)	$	(0.20)	$	0.24	$	(0.13)	$	0.21

	Six Months Ended		Six Months Ended		Nine Months Ended		Nine Months Ended
	March 31, 2020		March 31, 2019		June 30, 2020		June 30, 2019
Revenue	$	52,983,433	$	82,806,171	$	80,359,211	$	125,502,807
Operating Income (Loss)		(27,093,848)		32,956,836		(43,039,711)		51,552,585
Net Income (Loss)		(22,509,298)		35,934,235		(36,120,511)		56,269,944
Net Income (Loss) per Share (Diluted)	$	(0.23)	$	0.37	$	(0.36)	$	0.58

The decrease in our Revenue during the three and ~~six~~nine months ended ~~March 31,~~June 30, 2020 was driven by the timing of progress achieved in completing our performance obligation from our agreements with Janssen and JJDC, which were executed in October ~~2018.~~2018; partially offset by the $20 million milestone revenue from Amgen for the initiation of phase 2 clinical study for AMG 890 (ARO-LPA). The increase in our Net Loss during the three and ~~six~~nine months ended ~~March 31,~~June 30, 2020 was driven by this decrease in Revenue and also increases in Research and Development and General and Administrative Expenses as our pipeline of clinical candidates has continued to increase.

Total revenue was ~~$23,528,853~~$27,375,778 for the three months ended ~~March 31,~~June 30, 2020 and ~~$48,148,275~~$42,696,636 for the three months ended ~~March 31,~~June 30, 2019. Total revenue was ~~$52,983,433~~$80,359,211 for the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and ~~$82,806,171~~$125,502,807 for the ~~six~~nine months ended ~~March 31,~~June 30, 2019. Revenue in the both periods is primarily related to the recognition of a portion of the ~~$252.5~~$252.6 million initial transaction price associated with our agreements with Janssen and JJDC as we achieved progress toward completing our performance obligation within those agreements.

On September 28, 2016, the Company entered into two Collaboration and License agreements, and a Common Stock Purchase Agreement with Amgen Inc., a Delaware corporation (“Amgen”). Under one of the license agreements (the “Second Collaboration and License Agreement” or “AMG 890 (ARO-LPA) Agreement”), Amgen has received a worldwide, exclusive license to Arrowhead’s novel, RNAi 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 license agreement (the “First Collaboration and License Agreement” or “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. In both agreements, Amgen is wholly responsible for clinical development and commercialization. Under the terms of the agreements taken together, the Company has received $35 million in upfront payments, $21.5 million in the form of an equity investment by Amgen in the Company’s Common Stock, and a $10 million milestone payment, and may receive up to $420 million in 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 AMG 890 (ARO-LPA) 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 substantially completed its performance obligations under the AMG 890 (ARO-LPA) 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, which will result in a $20 million milestone payment to the Company. During the three ~~and six~~ months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized $20 million and $0 million of Revenue associated with its agreements with ~~Amgen.~~Amgen, respectively. During the ~~three and six~~nine months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized $20 million and $0.3 million of Revenue associated with its agreements with ~~Amgen.~~Amgen, respectively. As of ~~March 31,~~June 30, 2020, there ~~was $0~~were $20 million in contract assets recorded as accounts receivable, and $0 contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets.

On October 3, 2018, the Company entered into a License Agreement (“Janssen License Agreement”) and a Research Collaboration and Option Agreement (“Janssen Collaboration Agreement”) with Janssen Pharmaceuticals, Inc. (“Janssen”) part of the Janssen Pharmaceutical Companies of Johnson & Johnson. The Company also entered into a Stock Purchase Agreement (“JJDC Stock Purchase Agreement”) with Johnson & Johnson Innovation-JJDC, Inc. (“JJDC”), a New Jersey corporation. 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 potentially curative therapy for patients with chronic hepatitis B virus infection. Beyond the Company’s ongoing Phase 1 / 2 study of JNJ-3989 (ARO-HBV), Janssen will be wholly responsible for clinical development and commercialization. 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 will not include candidates in the Company’s current pipeline. The Company will perform discovery, optimization and preclinical research and development, entirely funded by Janssen, 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 million as an upfront payment, $75 million in the form of an equity investment by JJDC in Arrowhead common stock, two $25 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 three additional targets covered under the Janssen Collaboration Agreement. The Company is further eligible to receive tiered royalties up to mid teens under the Janssen License Agreement and up to low teens under the Janssen Collaboration Agreement on product sales.

The Company has evaluated these agreements in accordance with the new revenue recognition requirements that became effective for the Company on October 1, 2018. The adoption of the new revenue standard did not have a material impact on the balances reported when evaluated under the superseded revenue standard. At the inception of these agreements, the Company has 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 ongoing Phase 1 /

2 study of JNJ-3989 (ARO-HBV) and the Company’s responsibility to ensure certain manufacturing of 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 will be accounted for if and when it is exercised.

transaction price to its one distinct performance obligation for the JNJ-3989 (ARO-HBV) license and the associated Janssen R&D Services. This revenue will be recognized using a proportional performance method (based on actual labor hours versus estimated total labor hours) beginning in October 2018 and ending as the Company’s efforts in overseeing the ongoing phase ~~1 /~~ 1/2 clinical trial are completed. During the three months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized approximately ~~$22.2~~$6.9 million and ~~$47.9~~$42.3 million of Revenue associated with its agreements with Janssen and JJDC, respectively.During the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized approximately ~~$50.9~~$57.9 million and ~~$82.5~~$124.8 million of Revenue associated with its agreements with Janssen and JJDC, respectively. As of ~~March 31,~~June 30, 2020, there were $0 in contract assets recorded as accounts receivable, and ~~$33.2~~$26.3 million of contract liabilities recorded as current deferred revenue on the Company’s Consolidated Balance Sheets. The ~~$33.2~~$26.3 million of current deferred revenue is driven by the upfront payment, the premium paid by JJDC for its equity investment in the Company, and the two $25 million milestone payments earned, net of revenue recognized to date.

Janssen has also selected the first of the three targets under the Janssen Collaboration Agreement, now referred to as ARO-JNJ1, and the Company has begun to conduct its discovery, optimization and preclinical research and development of ARO-JNJ1. All costs and labor hours spent by the Company will be entirely funded by Janssen. During the three months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized ~~$1.4~~approximately $0.4 million and $0$0.4 million of Revenue associated with its efforts on the ARO-JNJ1 candidate, respectively. During the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019, the Company recognized ~~$2.1~~$2.4 million and $0$0.4 million of Revenue associated with these efforts on the ARO-JNJ1 candidate, respectively. As of ~~March 31,~~June 30, 2020, there were ~~$1.3~~$1.7 million of ~~contract~~contract assets recorded as accounts receivable, and $0 of contract liabilities recorded as ~~curren~~tcurrent deferred revenue on the Company’s Consolidated Balance Sheets.

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~~nine months ended ~~March 31,~~June 30, 2020 and 2019 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 ~~facility~~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 depreciation on lab equipment and leasehold improvements at our Madison research facility. The following table provides details of research and development 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, 2020		Category			March 31, 2019		Category			$			%			June 30, 2020		Category			June 30, 2019		Category			$		%
Salaries	$	4,216		14	%	$	3,387		16	%	$	829			24	%	$	4,861		15	%	$	3,456		18	%	$	1,405		41	%
Stock compensation		2,953		10	%		881		4	%		2,072			235	%		5,296		16	%		931		5	%		4,365		469	%
In Vivo studies		776		3	%		413		2	%		363			88	%		810		3	%		766		4	%		44		6	%
Drug manufacturing		7,377		25	%		7,430		36	%		(53	)		-1	%		6,607		20	%		4,907		25	%		1,700		35	%
Toxicity/efficacy studies		2,171		7	%		2,410		12	%		(239	)		-10	%		3,019		9	%		1,858		10	%		1,161		62	%
Clinical trials		5,268		18	%		3,205		15	%		2,063			64	%		6,129		19	%		4,310		22	%		1,819		42	%
License, royalty & milestones		900		3	%		-		0	%		900		N/A				-		0	%		-		0	%		-	N/A
Facilities related		823		3	%		783		4	%		40			5	%		1,209		4	%		652		3	%		557		85	%
Depreciation/amortization		1,219		4	%		1,170		6	%		49			4	%		1,382		4	%		998		5	%		384		38	%
Other R&D		3,740		13	%		1,120		5	%		2,620			234	%		3,260		10	%		1,414		7	%		1,846		131	%
Total	$	29,443		100	%	$	20,799		100	%	$	8,644			42	%	$	32,573		100	%	$	19,292		100	%	$	13,281		69	%

	Six					Six											Nine					Nine
	Months Ended		% of Expense			Months Ended		% of Expense			Increase (Decrease)						Months Ended		% of Expense			Months Ended		% of Expense			Increase (Decrease)
	March 31, 2020		Category			March 31, 2019		Category			$			%			June 30, 2020		Category			June 30, 2019		Category			$		%
Salaries	$	8,312		16	%	$	6,664		17	%	$	1,648			25	%	$	13,173		15	%	$	10,121		18	%	$	3,052		30	%
Stock compensation		4,115		8	%		1,522		4	%		2,593			170	%		9,411		11	%		2,453		4	%		6,958		284	%
In Vivo studies		1,747		3	%		896		2	%		851			95	%		2,557		3	%		1,661		3	%		896		54	%
Drug manufacturing		12,485		24	%		13,234		35	%		(749	)		-6	%		19,092		22	%		18,141		32	%		951		5	%
Toxicity/efficacy studies		6,123		12	%		4,821		13	%		1,302			27	%		9,142		11	%		6,679		12	%		2,463		37	%
Clinical trials		9,635		18	%		5,447		14	%		4,188			77	%		15,764		19	%		9,756		17	%		6,008		62	%
License, royalty & milestones		903		2	%		-		0	%		903		N/A				903		1	%		-		0	%		903	N/A
Facilities related		1,444		3	%		1,366		4	%		78			6	%		2,653		3	%		2,018		4	%		635		31	%
Depreciation/amortization		2,330		4	%		2,342		6	%		(12	)		-1	%		3,712		4	%		3,340		6	%		372		11	%
Other R&D		5,723		11	%		2,079		5	%		3,644			175	%		8,983		11	%		3,493		6	%		5,490		157	%
Total	$	52,817		100	%	$	38,371		100	%	$	14,446			38	%	$	85,390		100	%	$	57,662		100	%	$	27,728		48	%

Salaries expense increased by ~~$829,000~~$1,405,000 from ~~$3,387,000~~$3,456,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$4,216,000~~$4,861,000 during the current period. Salaries expense increased by ~~$1,648,000~~$3,052,000 from ~~$6,664,000~~$10,121,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$8,312,000~~$13,173,000 during the current period. The increase in the expense is primarily due to an increase in R&D headcount that has occurred as the Company has expanded its pipeline of candidates.

Stock compensation expense, a non-cash expense, increased by ~~$2,072,000~~$4,365,000 from ~~$881,000~~$931,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$2,953,000~~$5,296,000 during the current period. Stock compensation expense, a non-cash expense, increased by ~~$2,593,000~~$6,958,000 from ~~$1,522,000~~$2,453,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$4,115,000~~$9,411,000 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 is primarily due to the increased headcount discussed above and a mix of higher grant date fair values of awards amortizing during the periods due to the Company’s stock price at the time of the grants.

In vivo studies expense increased by ~~$363,000~~$44,000 from ~~$413,000~~$766,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$776,000~~$810,000 during the current period. In vivo studies expense increased by ~~$851,000~~$896,000 from ~~$896,000~~$1,661,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$1,747,000~~$2,557,000 during the current period. In vivo studies expense can vary depending on the stage of preclinical candidates, the nature and amount of testing required and the cost variation of different in vivo testing models. The increase in vivo studies expense is the result of the timing of discovery studies being completed between periods.

Drug manufacturing expense ~~decreased~~increased by ~~$53,000~~$1,700,000 from ~~$7,430,000~~$4,907,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$7,377,000~~$6,607,000 during the current period. Drug manufacturing expense ~~decreased~~increased by ~~$749,000~~$951,000 from ~~$13,234,000~~$18,141,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$12,485,000~~$19,092,000 during the current period. The ~~decrease~~increase in the expense primarily relates to the timing of manufacturing campaigns in preparation for our candidate clinical trials and toxicology studies. We anticipate this expense to increase as the volume of candidates in our pipeline increases and as each candidate progresses through clinical trial phases.

Toxicity/efficacy studies expense ~~decreased~~increased by ~~$239,000~~$1,161,000 from ~~$2,410,000~~$1,858,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$2,171,000~~$3,019,000 during the current period. Toxicity/efficacy studies expense increased by ~~$1,302,000~~$2,463,000 from ~~$4,821,000~~$6,679,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$6,123,000~~$9,142,000 during the current period. This category includes IND-enabling toxicology studies as well as post-IND toxicology studies, such as long-term toxicology studies, and other efficacy studies. The change in the expense primarily relates to toxicology studies for ARO-ANG3, ARO-APOC3, ARO-HIF2 and ARO-HSD as each candidate progresses through and into clinical trials. We anticipate this expense to increase as we prepare to enter clinical trials with our other drug candidates.

Clinical trials expense increased by ~~$2,063,000~~$1,819,000 from ~~$3,205,000~~$4,310,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$5,268,000~~$6,129,000 during the current period. Clinical trials expense increased by ~~$4,188,000~~$6,008,000 from ~~$5,447,000~~$9,756,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$9,635,000~~$15,764,000 during the current period. The increase in the expense is primarily due to the ongoing ARO-AAT and JNJ-3989 (ARO-HBV) clinical trials, ~~and~~ the progression of the ARO-ANG3 and ARO-APOC3 clinical trials, and the start up of the ARO-HSD, ARO-HIF2 and ~~ARO-HIF2~~ARO-ENaC clinical trials. We anticipate this expense to increase as our current clinical candidates progress through clinical trials and as we enter clinical trials with our other drug candidates.

License, royalty and milestones expense ~~increased by $900,000~~did not change from $0 during the three months ended ~~March 31,~~June 30, 2019 to ~~$900,000~~$0 during the current period. License, royalty and milestones expense increased by $903,000 from $0 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to $903,000 during the current period. This category includes milestone payments which can vary from period to period depending on the nature of our various license agreements, and the timing of reaching various development milestones requiring payment. During the ~~three and six~~nine months ended ~~March 31,~~June 30, 2020, the Company accrued a $0.9 million milestone payment related to the progression of the ARO-ENaC program. During the ~~three and six~~nine months ended ~~March 31,~~June 30, 2019, the Company did not accrue for any milestone payments.

Facilities expense increased by ~~$40,000~~$557,000 from ~~$783,000~~$652,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$823,000~~$1,209,000 during the current period. Facilities expense increased by ~~$78,000~~$635,000 from ~~$1,366,000~~$2,018,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$1,444,000~~$2,653,000 during the current ~~period~~period. This category includes rental costs for our research and development ~~facility~~facilities in Madison, ~~Wisconsin.~~Wisconsin and San Diego, California. The increase in the expense is primarily due ~~to increased rental and common area maintenance expenses for~~the commencement of our ~~research and development facility.~~sublease in San Diego, California in April 2020.

Depreciation and amortization expense, a non-cash expense, increased by ~~$49,000~~$384,000 from ~~$1,170,000~~$998,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$1,219,000~~$1,382,000 during the current period. Depreciation and amortization expense, a non-cash expense, ~~decreased~~increased by ~~$12,000~~$372,000 from ~~$2,342,000~~$3,340,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$2,330,000~~$3,712,000 during the current period. The majority of depreciation and amortization expense relates to depreciation on lab equipment and leasehold improvements at our Madison research facility. In addition, the Company records depreciation on leasehold improvements at its Madison research facility. Depreciation and amortization expense was relatively consistent in both the three month and six month periods.

Other research expense increased by ~~$2,620,000~~$1,846,000 from ~~$1,120,000~~$1,414,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$3,740,000~~$3,260,000 during the current period. Other research expense increased by ~~$3,644,000~~$5,490,000 from ~~$2,079,000~~$3,493,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$5,723,000~~$8,983,000 during the current period. This category includes the following costs to support discovery efforts and the advancement of current drug candidates: in-house laboratory supplies, outsourced labs services, and other miscellaneous research and development expenses. The increase in other research expense is due to additional in-house laboratory supplies for our increased headcount and partially due to equipment purchased for the new San Diego research and development facility.

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, 2020		Category			March 31, 2019		Category			$		%			June 30, 2020		Category			June 30, 2019		Category			$		%
Salaries	$	3,033		19	%	$	1,579		30	%	$	1,454		92	%	$	2,633		25	%	$	1,241		26	%	$	1,392		112	%
Stock compensation		10,019		61	%		1,720		32	%		8,299		483	%		4,750		44	%		1,027		21	%		3,723		363	%
Professional/outside services		1,677		10	%		1,362		26	%		315		23	%		2,020		19	%		1,670		35	%		350		21	%
Facilities related		418		3	%		265		5	%		153		58	%		446		4	%		241		5	%		205		85	%
Depreciation/amortization		153		1	%		6		0	%		147		2450	%		154		1	%		5		0	%		149		2980	%
Other G&A		1,026		6	%		407		8	%		619		152	%		746		7	%		625		13	%		121		19	%
Total	$	16,326		100	%	$	5,339		100	%	$	10,987		206	%	$	10,749		100	%	$	4,809		100	%	$	5,940		123	%

	Six					Six										Nine					Nine
	Months Ended		% of Expense			Months Ended		% of Expense			Increase (Decrease)					Months Ended		% of Expense			Months Ended		% of Expense			Increase (Decrease)
	March 31, 2020		Category			March 31, 2019		Category			$		%			June 30, 2020		Category			June 30, 2019		Category			$		%
Salaries	$	7,114		26	%	$	3,667		32	%	$	3,447		94	%	$	9,747		26	%	$	4,909		30	%	$	4,838		99	%
Stock compensation		13,349		49	%		3,797		33	%		9,552		252	%		18,099		48	%		4,824		30	%		13,275		275	%
Professional/outside services		3,499		13	%		2,581		23	%		918		36	%		5,519		15	%		4,252		26	%		1,267		30	%
Facilities related		1,211		4	%		563		5	%		648		115	%		1,657		4	%		803		5	%		854		106	%
Depreciation/amortization		302		1	%		11		0	%		291		2645	%		456		1	%		16		0	%		440		2750	%
Other G&A		1,785		7	%		860		8	%		925		108	%		2,531		7	%		1,484		9	%		1,047		71	%
Total	$	27,260		100	%	$	11,479		100	%	$	15,781		137	%	$	38,009		100	%	$	16,288		100	%	$	21,721		133	%

Salaries expense increased by ~~$1,454,000~~$1,392,000 from ~~$1,579,000~~$1,241,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$3,033,000~~$2,633,000 during the current period. Salaries expense increased by ~~$3,447,000~~$4,838,000 from ~~$3,667,000~~$4,909,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$7,114,000~~$9,747,000 during the current period. The increase in the expense is primarily driven by annual merit increases, performance bonuses and increased headcount.

Stock compensation expense, a non-cash expense, increased by ~~$8,299,000~~$3,723,000 from ~~$1,720,000~~$1,027,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$10,019,000~~$4,750,000 during the current period. Stock compensation expense, a non-cash expense, increased by ~~$9,552,000~~$13,275,000 from ~~$3,797,000~~$4,824,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$13,349,000~~$18,099,000 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 expense is primarily due to the timing of the achievement of certain performance-based awards in each ~~period.~~period and a mix of higher grant date fair values of awards amortizing during the periods due to the Company’s stock price at the time of the grants.

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 ~~$315,000~~$350,000 from ~~$1,362,000~~$1,670,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$1,677,000~~$2,020,000 during the current period. Professional/outside services expense increased by ~~$918,000~~$1,267,000 from ~~$2,581,000~~$4,252,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$3,499,000~~$5,519,000 during the current period. The increases in the expense in the three and ~~six~~nine month periods are primarily related ~~to recruiting fees for increased headcount.~~ certain patent-related expenses.

Facilities-related expense increased by ~~$153,000~~$205,000 from ~~$265,000~~$241,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$418,000~~$446,000 during the current period. Facilities-related expense increased by ~~$648,000~~$854,000 from ~~$563,000~~$803,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$1,211,000~~$1,657,000 during the current period. This category primarily includes rental costs for our corporate headquarters in Pasadena, California. The increase in the expense is primarily related to costs incurred as we moved into our new corporate headquarters during the current period.

Depreciation and amortization expense, a noncash expense, increased by ~~$147,000~~$149,000 from ~~$6,000~~$5,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$153,000~~$154,000 during the current period. Depreciation and amortization expense, a noncash expense, increased by ~~$291,000~~$440,000 from ~~$11,000~~$16,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$302,000~~$456,000 during the current period. ~~The majority of general and administrative depreciation and amortization expense relates to depreciation on leasehold improvements at our Pasadena headquarters.~~ The increase in the expense is primarily related to amortization of leasehold improvements for our new corporate headquarters.

Other G&A expense increased by ~~$619,000~~$121,000 from ~~$407,000~~$625,000 during the three months ended ~~March 31,~~June 30, 2019 to ~~$1,026,000~~$746,000 during the current period. Other G&A expense increased by ~~$925,000~~$1,047,000 from ~~$860,000~~$1,484,000 during the ~~six~~nine months ended ~~March 31,~~June 30, 2019 to ~~$1,785,000~~$2,531,000 during the current period. This category consists primarily of travel, communication and technology, office expenses, and franchise and property tax expenses. The increase in the expense was due to increased communication and technology and office expenses associated with our new corporate headquarters.

Other income / expense was income of ~~$2,404,685~~$2,334,649 and ~~$1,886,290~~$1,739,959 during the three months ended ~~March 31,~~June 30, 2020 and 2019, respectively. Other income / expense was income of ~~$4,584,550~~$6,919,200 and ~~$2,977,399~~$4,717,359 during the ~~six~~nine months ended ~~March 31,~~June 30, 2020 and 2019, respectively. Other income / expense in the both periods was interest income earned on the Company’s investments. This interest income has increased in the current periods as our investment holdings have grown.

Arrowhead has historically financed its operations through the sale of its equity securities. Research and development activities have required significant capital investment since the Company’s inception and are expected to continue to require significant cash expenditure in the future.

At ~~March 31,~~June 30, 2020, the Company had cash on hand of approximately ~~$256.7~~$219.3 million as compared to $221.8 million at September 30, 2019. Excess cash invested in short-term fixed income securities was ~~$51.0~~$67.7 million at ~~March 31,~~June 30, 2020, compared to $36.9 million at September 30, 2019. Excess cash invested in long-term fixed income securities was ~~$190.6~~$177.5 million at ~~March 31,~~June 30, 2020, compared to $44.2 million at September 30, 2019. 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~~nine months ended ~~March 31,~~June 30, 2020 and 2019 is as follows:

During the ~~six~~nine months ended ~~March 31,~~June 30, 2020, the Company used ~~$51.1~~$84.5 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 in investing activities was ~~$168.8~~$174.9 million, which was primarily related to the purchase of fixed-income investments of ~~$180.5~~$194.0 million and property and equipment of ~~$7.9~~$10.1 million, partially offset by maturities of fixed-income securities of ~~$19.6~~$29.1 million. Cash provided by financing activities of ~~$254.8~~$256.9 million was driven by the securities financing in December 2019, which generated $250.5 million in net cash proceeds, as well as ~~$4.3~~$6.5 million in cash received from stock option exercises.

During the ~~six~~nine months ended ~~March 31,~~June 30, 2019, the Company generated ~~$148.7~~$159.2 million in cash from operating activities, which was primarily related to the $175.0 million upfront payment and the $25.0 million milestone payment received from Janssen, and the premium JJDC paid on the Company’s common stock during the period. These inflows were partially offset by approximately ~~$41~~$55 million of cash used for the ongoing expenses of the Company’s research and development programs and general and administrative expenses. Cash used in investing activities was ~~$79.0~~$64.6 million, which was primarily related to purchases of fixed-income investments of $90.3 million partially offset by maturities of fixed-income investments of $30.0 million. Cash provided by financing activities of ~~$61.8~~$64.5 million was driven by the equity investment the Company received from JJDC during the period.

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, 2019.

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 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 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 legal proceedings in Part I, Item 3 of our Annual Report on Form 10-K for the year ended September 30, 2019.

The disclosure below supplements the risk factors described in our Annual Report on Form 10-K for the year ended September 30, 2019. 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, 2019, 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.

Our results of operations and financial condition may be adversely affected by the novel coronavirus (COVID-19) pandemic and other public health epidemics.

Our business and its operations, including but not limited to our research and development activities and our supply chain, could be adversely affected by health epidemics in regions where we have business operations, and such health epidemics could cause significant disruption in the operations of third parties upon whom we rely. In December 2019, a novel strain of coronavirus, SARS-CoV-2, causing a disease referred to as COVID-19, was reported to have surfaced in Wuhan, China. Since then, COVID-19 has spread to other countries, including the United States, and has been declared a pandemic by the World Health Organization. In response to public health directives and orders related to COVID-19, we have implemented work-from-home policies for substantially all of our employees to the extent work can be performed effectively at home. The effects of executive and similar government orders, shelter-in-place orders and our work-from-home policies may negatively impact our productivity, disrupt our business, increase our expenses, including costs associated with preventive and precautionary measures that we, companies with which we conduct business, and governments are taking, and delay our clinical trials and timelines, the magnitude of which will depend, in part, on the length and severity of the restrictions and other limitations on our ability to conduct our business in the ordinary course. These and similar, and perhaps more severe, disruptions in our operations could negatively impact our business, results of operations and financial condition.

Quarantines, shelter-in-place, executive and similar government orders, or the perception that such orders, shutdowns or other restrictions on the conduct of business operations could occur, related to COVID-19 or other infectious diseases, have impacted and may continue to impact personnel at our business partners in the United States and other countries, or our access to raw materials for our research and development facility discovery efforts, which would disrupt our supply chain.

In addition, our clinical trials have been and may continue to be affected by the COVID-19 pandemic. For example, during fiscal year 2020, we ~~have~~temporarily paused enrollment in our two ARO-AAT studies: SEQUOIA and the ARO-AAT 2002 study. As of June 30, 2020, enrollment in both of these studies has resumed. Additional delays have occurred in the Company’s earlier stage programs, but we do not expect a material impact to any program’s anticipated timelines. Several of the Company’s other clinical candidates are in the start-up stage (ARO-HSD, ARO-HIF2 and ARO-ENaC), during which significant clinical costs will continue to be incurred. If COVID-19 continues to spread in the United States and elsewhere, we may experience additional disruptions that could severely impact our business, preclinical studies and clinical trials, including:

The spread of COVID-19, which has caused a broad impact globally, may materially affect us economically. While the potential economic impact brought by COVID-19, and the duration of such impact, may be difficult to assess or predict, the widespread pandemic has resulted in significant disruption of global financial markets, which could reduce our ability to access capital and negatively affect our future liquidity. In addition, a recession or market correction resulting from the spread of COVID-19 and related government orders and restrictions could materially affect our business and the value of our common stock.

The COVID-19 pandemic continues to evolve rapidly. The ultimate impact of the COVID-19 pandemic or a similar public health emergency is highly uncertain and subject to change. We do not yet know the full extent of potential delays or impacts on our business, our clinical trials, healthcare systems, or the global economy as a whole. However, any one or a combination of these events could have an adverse effect on our results of operations and financial ~~condition~~condition.

Effective August 5, 2020, we entered into an Open Market Sale Agreement (the “ATM Agreement”), pursuant to which we may, from time to time, sell up to $250,000,000 in shares of our common stock through Jefferies, acting as the sales agent and/or principal, in an ATM Offering. We are not required to sell shares under the ATM Agreement. We will pay Jefferies a commission of up to 3.0% of the aggregate gross proceeds we receive from all sales of our 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. No sales have been made under the ATM Agreement.

The ATM Offering is being made under a prospectus supplement filed on August 5, 2020, and related prospectus filed with the SEC pursuant to our automatically effective shelf registration statement on Form S-3 (File No. 333-235324), filed with the SEC on December 2, 2019.

A copy of the ATM Agreement is attached as Exhibit 1.1 to this Quarterly Report. The foregoing description of the ATM Agreement does not purport to be complete and is qualified in its entirety by reference to Exhibit 1.1. A copy of the opinion of Gibson, Dunn & Crutcher LLP relating to the validity of the securities issued in the ATM Offering is filed as Exhibit 5.1 to this Quarterly Report.

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 of incorporation)		(I.R.S. Employer Identification No.)


Securities registered pursuant to Section 12(b) of the Act:
Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common Stock, Par Value $0.001 per share	ARWR	The Nasdaq Global Select Market

	Page(s)
PART I — FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS (unaudited)	1

Consolidated Balance Sheets	1

Consolidated Statements of Operations and Comprehensive Income (Loss)	2

Consolidated Statement of Stockholders’ Equity	3

Consolidated Statements of Cash Flows	54

Notes to Consolidated Financial Statements	65

ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS	1615

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK	2624

ITEM 4. CONTROLS AND PROCEDURES	2624

PART II — OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS	2725

ITEM 1A. RISK FACTORS	2725

ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS	2826

ITEM 3. DEFAULTS UPON SENIOR SECURITIES	2826

ITEM 4. MINE SAFETY DISCLOSURES	2826

ITEM 5. OTHER INFORMATION	2826

ITEM 6. EXHIBITS	2928

SIGNATURE	3029

Exhibit Number		Document Description

~~10.1~~ ~~31.1~~1.1		~~Sublease agreement~~Open Market Sale Agreement, dated as of August 5, 2020, by and between ~~Halozyme, Inc. and~~ Arrowhead Pharmaceuticals, Inc. ~~dated March 3, 2020~~and Jefferies LLC**†

5.1		Opinion of Gibson, Dunn, and Crutcher, LLP*

31.1		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*

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*

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**

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**

101.SCH ~~101.CAL~~ ~~101.LAB~~ ~~101.PRE~~ ~~101.DEF~~ ~~104~~		XBRL Taxonomy Extension Schema Document*

101.CAL		XBRL Taxonomy Extension Calculation Linkbase Document*

101.LAB		XBRL Taxonomy Extension Label Linkbase Document*

101.PRE		XBRL Taxonomy Extension Presentation Linkbase Document*

101.DEF		XBRL Taxonomy Extension Definition Linkbase Document*

104		The cover page from the Company’s Quarterly Report on Form 10-Q for the quarter ended ~~March 31,~~June 30, 2020, formatted in Inline XBRL (included as Exhibit 101)*

ARROWHEAD PHARMACEUTICALS, INC.

By:		/s/ Kenneth A. Myszkowski
		Kenneth A. Myszkowski
		Chief Financial Officer

	As of September 30, 2019
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Fair Value
Commercial notes (due within one year)	$	36,899,894	$	222,584	$	—	$	37,122,478
Commercial notes (due within one through three years)	$	44,175,993	$	875,258	$	—	$	45,051,251
Total	$	81,075,887	$	1,097,842	$	—	$	82,173,729

2020	$	1,521,451
2021		2,256,379
2022		2,521,446
2023		2,590,558
2024		2,661,512
2025 and thereafter		10,834,206
Total	$	22,385,552


	Nine Months Ended June 30, 2020			Nine Months Ended June 30, 2019
Cash Flow from Continuing Operations:
Operating Activities	$	(84,541,545	)	$	159,225,017
Investing Activities		(174,883,363)			(64,575,067	)
Financing Activities		256,943,397			64,548,584
Net Increase (Decrease) in Cash		(2,481,511)			159,198,534
Cash and Cash Equivalents at Beginning of Period		221,804,128			30,133,213
Cash and Cash Equivalents at End of Period	$	219,322,617		$	189,331,747


	Six Months Ended March 31, 2020			Six Months Ended March 31, 2019
Cash Flow from Continuing Operations:
Operating Activities	$	(51,114,395	)	$	148,698,255
Investing Activities		(168,849,557)			(78,973,570	)
Financing Activities		254,810,551			61,781,310
Net Increase (Decrease) in Cash		34,846,599			131,505,995
Cash and Cash Equivalents at Beginning of Period		221,804,128			30,133,213
Cash and Cash Equivalents at End of Period	$	256,650,727		$	161,639,208

Large Accelerated Filer

Accelerated Filer

Non-Accelerated Filer

Smaller Reporting Company

Emerging Growth Company