UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

FORM 10-Q

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

For the quarterly period ended ~~June 30, 2019~~March 31, 2020

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

For the transition period from to

Commission File Number: 001-36289

_______________________________________________________

Genocea Biosciences, Inc.

(Exact Name of Registrant as Specified in Its Charter)



Delaware		51-0596811
(State or Other Jurisdiction of Incorporation or Organization)		(IRS Employer Identification No.)



100 Acorn Park Drive
Cambridge, Massachusetts		02140
(Address of Principal Executive Offices)		(Zip Code)

Registrant’s Telephone Number, Including Area Code: (617) 876-8191

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, $0.001 par value per share	GNCA	NASDAQ Capital Market

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes x 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 x No ¨

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



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

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. x¨

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

As of ~~July 23, 2019,~~April 28, 2020, there were ~~26,149,689~~27,643,773 shares of the registrant’s Common Stock, par value $0.001 per share, outstanding.

FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q contains forward-looking statements that involve substantial risks and uncertainties. Forward-looking statements are neither historical facts nor assurances of future performance. Instead, they are based on our current beliefs, expectations and assumptions regarding the future of our business, future plans and strategies, our clinical results and other future conditions. The words “anticipate”, “believe”, “contemplate”, “continue”, “could”, “estimate”, “expect”, “forecast”, “goal”, “intend”, “may”, “plan”, “potential”, “predict”, “project”, “should”, “target”, “will”, “would”, or the negative of these terms or other similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words.

Any forward-looking statements in this Quarterly Report on Form 10-Q reflect our current views with respect to future events or to our future financial performance and involve known and unknown risks, uncertainties and other factors that may cause our actual results, performance or achievements to be materially different from any future results, performance or achievements expressed or implied by these forward-looking statements. Factors that may cause actual results to differ materially from current expectations include, among other things, those listed in our Annual Report on Form 10-K and other filings with the Securities Exchange Commission (the “SEC”), including the following:

our estimates regarding the timing and amount of funds we require to conduct clinical trials for GEN-009, to continue preclinical studies and file an investigational new drug (“IND”) for GEN-011, to continue preclinical studies for our other product candidates and to continue our investments in immuno-oncology;

our estimates regarding expenses, future revenues, capital requirements, the sufficiency of our current and expected cash resources and our need for additional financing;

the timing of, and our ability to, obtain and maintain regulatory approvals for our product candidates;

the availability of materials and equipment, and the potential disruptions in supply chains resulting from the international public health emergency associated with the novel coronavirus (COVID-19);

the potential benefits of strategic partnership agreements and our ability to enter into strategic partnership arrangements;

our intellectual property position;

the rate and degree of market acceptance and clinical utility of any approved product candidate;

our ability to quickly and efficiently identify and develop product candidates; and

our commercialization, marketing and manufacturing capabilities and ~~strategy.~~strategies.

We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements, and you should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements we make. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, joint ventures or investments we may make or collaborations or strategic partnerships we may enter into. Except as required by law, we assume no obligation to update or revise these forward-looking statements for any reason, even if new information becomes available in the future.

This Quarterly Report on Form 10-Q includes statistical and other industry and market data that we obtained from industry publications and research, surveys and studies conducted by third parties. Industry publications and third-party research, surveys and studies generally indicate that their information has been obtained from sources believed to be reliable, although they do not guarantee the accuracy or completeness of such information. While we believe these industry publications and third-party research, surveys and studies are reliable, we have not independently verified such data.

Genocea Biosciences, Inc.

Form 10-Q

For the Quarter Ended ~~June 30, 2019~~March 31, 2020

TABLE OF CONTENTS



		Page
PART I. FINANCIAL INFORMATION		4
Item 1.	Financial Statements (unaudited)	4
	Condensed Consolidated Balance Sheets as of ~~June 30, 2019~~March 31, 2020 and December 31, ~~2018~~2019	4
	Condensed Consolidated Statements of Operations and Comprehensive Loss for the three ~~and six~~ months ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~	5
	Condensed Consolidated Statements of Stockholders' Equity for the three ~~and six~~ months ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~	6
	Condensed Consolidated Statements of Cash Flows for the ~~six~~three months ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~	7
	Notes to Unaudited Condensed Consolidated Financial Statements	8
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	1918
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	2624
Item 4.	Controls and Procedures	2624

PART II. OTHER INFORMATION		2725
Item 11.	Legal Proceedings	2725
Item 1A.	Risk Factors	28
~~Item 5.~~	~~Other Information~~	2825
Item 6.	Exhibits	2826

PART I. FINANCIAL INFORMATION

Item 1. Financial Statements

Genocea Biosciences, Inc.

Condensed Consolidated Balance Sheets

(unaudited)

(in thousands)


	June 30, 2019			December 31, 2018			March 31, 2020			December 31, 2019
Assets
Current assets:
Cash and cash equivalents	$	58,670		$	26,361		$	26,509		$	40,127
Prepaid expenses and other current assets	1,062			696			2,562			1,457
Total current assets	59,732			27,057			29,071			41,584
Property and equipment, net	2,813			2,582			2,474			2,617
Operating lease right-of-use asset	6,840			—
Right of use assets							11,782			6,306
Restricted cash	316			316			631			631
Other non-current assets	1,061			1,160			1,234			1,473
Total assets	$	70,762		$	31,115		$	45,192		$	52,611

Liabilities and stockholders’ equity
Current liabilities:
Accounts payable	$	1,247		$	1,659		$	860		$	553
Accrued expenses and other current liabilities	5,050			3,816			4,077			4,611
Operating lease liabilities	1,045			—
Lease liabilities							2,028			1,117
Current portion of long-term debt	2,673			5,257			7,700			—
Total current liabilities	10,015			10,732			14,665			6,281
Non-current liabilities:
Long-term debt, net of current portion							5,815			13,407
Warrant liability	5,389			3,472			1,705			2,486
Long-term debt, net of current portion and discount	11,059			9,565
Operating lease liabilities, net of current portion	5,861			—
Other non-current liabilities	—			11
Lease liabilities, net of current portion							9,994			5,395
Total liabilities	32,324			23,780			32,179			27,569
Commitments and contingencies (Note 9)
Commitments and contingencies (Note 5)
Stockholders’ equity:
Preferred stock	701			701
Common stock	26			11
Preferred stock, $0.001 par value; (shares authorized of 25,000,000 at March 31, 2020 and December 31, 2019; 1,635 shares issued and outstanding at March 31, 2020 and December 31, 2019)							701			701
Common stock, $0.001 par value; (shares authorized of 85,000,000 at March 31, 2020 and December 31, 2019, 27,643,773 shares issued and outstanding at March 31, 2020 and 27,452,900 shares issued and outstanding at December 31, 2019)							28			27
Additional paid-in capital	351,777			298,627			356,091			355,268
Accumulated deficit	(314,066		)	(292,004		)	(343,807		)	(330,954		)
Total stockholders’ equity	38,438			7,335			13,013			25,042
Total liabilities and stockholders’ equity	$	70,762		$	31,115		$	45,192		$	52,611

See accompanying notes to unaudited condensed consolidated financial statements.

Genocea Biosciences, Inc.

Condensed Consolidated Statements of Operations and Comprehensive Loss

(unaudited)

(in thousands, except per share data)


	Three Months Ended June 30,						Six Months Ended June 30,						Three Months Ended March 31,
	2019			2018			2019			2018			2020			2019
Operating expenses:
Research and development	$	6,849		$	5,316		$	13,309		$	12,591		$	9,987		$	6,460
General and administrative	3,217			4,472			6,234			7,581			3,388			3,017
Total operating expenses	10,066			9,788			19,543			20,172			13,375			9,477
Loss from operations	(10,066		)	(9,788		)	(19,543		)	(20,172		)	(13,375		)	(9,477		)
Other income (expense):
Change in fair value of warrants	3,870			5,498			(1,917		)	199			781			(5,787		)
Interest expense, net	(299		)	(241		)	(601		)	(442		)	(259		)	(302		)
Other income (expense)	—			93			(1		)	87			—			(1		)
Total other income (expense)	3,571			5,350			(2,519		)	(156		)	522			(6,090		)
Net loss	$	(6,495	)	$	(4,438	)	$	(22,062	)	$	(20,328	)	$	(12,853	)	$	(15,567	)

Comprehensive loss	$	(6,495	)	$	(4,438	)	$	(22,062	)	$	(20,328	)	$	(12,853	)	$	(15,567	)
Net loss per share - basic and diluted	$	(0.42	)	$	(0.42	)	$	(1.57	)	$	(2.07	)	$	(0.46	)	$	(1.22	)
Weighted-average number of common shares used in computing net loss per share	15,344			10,693			14,035			9,804			28,141			12,713

See accompanying notes to unaudited condensed consolidated financial statements.

Genocea Biosciences, Inc.

Condensed Consolidated Statements of Stockholders' Equity ~~(Deficit)~~

(unaudited)

(in thousands)


				Preferred Shares Amount			Additional Paid-In Capital			Accumulated Deficit				Total Stockholders' Equity									Preferred Shares Amount			Additional Paid-In Capital			Accumulated Deficit				Total Stockholders' Equity
	Common Shares								Common Shares
	Shares	Amount							Shares								Amount
Balance at December 31, 2018	10,847	$	11			$	701		$				298,627				$	(292,004	)	$	7,335
Balance at December 31, 2019																		27,453		$	27		$	701		$	355,268		$	(330,954	)		$	25,042
Issuance of common stock, net	3,200	3				—			14,023				—				14,026			187		1			—			439				—				440
Exercise of stock options	3	—		—			12				—				12
Stock-based compensation expense	—	—		—			429			—				429				—		—			—			384			—				384
Issuance of common stock under employee benefit plans																		4		—			—			—			—				—
Net loss	—	—		—			—			(15,567		)		(15,567		)		—		—			—			—			(12,853		)		(12,853		)
Balance at March 31, 2019	14,050	$	14	$	701		$	313,091		$	(307,571	)		$	6,235
Issuance of common stock, net	12,074	12		—			38,155			—				38,167
Issuance of common stock; ESPP purchase	24	—		—			48			—				48
Exercise of stock options	2	—		—			9			—				9
Stock-based compensation expense	—	—		—			474			—				474
Net loss	—	—		—						(6,495		)		(6,495		)
Balance at June 30, 2019	26,150	$	26	$	701		$	351,777		$	(314,066	)		$	38,438
Balance at March 31, 2020																		27,644		$	28		$	701		$	356,091		$	(343,807	)		$	13,013

Preferred Shares Amount Additional Paid-In Capital Accumulated Deficit Total Stockholders' Equity (Deficit)
Common Shares
Shares Amount
Balance at December 31, 2017 3,592
$ 3
$ —
$ 258,140
$ (264,193 ) $ (6,050 )
Issuance of common stock, net 6,790
7
701
35,156
—
35,864
Stock-based compensation expense —
—
—
644
—
644
Net loss —
—
—
—
(15,890 ) (15,890 )
Balance at March 31, 2018 10,382
$ 10
$ 701
$ 293,940
$ (280,083 ) $ 14,568
Issuance of common stock, net 440
1
—
2,921
—
2,922
Issuance of common stock; ESPP purchase 6
—
—
31
—
31
Issuance of Warrants on Debt Modification —
—
—
190
—
190
Stock-based compensation —
—
—
592
—
592
Net loss —
—
—
—
(4,438 ) (4,438 )
Balance at June 30, 2018 10,828
$ 11
$ 701
$ 297,674
$ (284,521 ) $ 13,865



				Preferred Shares Amount		Additional Paid-In Capital		Accumulated Deficit			Total Stockholders' Equity
	Common Shares
	Shares	Amount
Balance at December 31, 2018	10,847	$	11	$	701	$	298,627	$	(292,004	)	$	7,335
Issuance of common stock, net	3,200	3		—		14,023		—			14,026
Exercise of stock options	3	—		—		12		—			12
Stock-based compensation expense	—	—		—		429		—			429
Net loss	—	—		—		—		(15,567		)	(15,567		)
Balance at March 31, 2019	14,050	$	14	$	701	$	313,091	$	(307,571	)	$	6,235

See accompanying notes to unaudited condensed consolidated financial statements.

Genocea Biosciences, Inc.

Condensed Consolidated Statements of Cash Flows

(unaudited)

(in thousands)


	Six Months Ended June 30,						Three Months Ended March 31,
	2019			2018			2020			2019
Operating activities
Net loss	$	(22,062	)	$	(20,328	)	$	(12,853	)	$	(15,567	)
Adjustments to reconcile net loss to net cash used in operating activities
Depreciation and amortization	550			543			276			272
Stock-based compensation	902			1,236			384			429
Allocation of proceeds to transaction expenses	—			2,115
Change in fair value of warrant liability	1,917			(2,315		)	(781		)	5,787
Gain on sale of equipment	(19		)	(50		)	(13		)	—
Write-off of deferred financing fees	—			355
Non-cash interest expense	41			291			109			162
Asset impairment							97			—
Changes in operating assets and liabilities	729			(5,222		)	(1,015		)	(1,382		)
Net cash used in operating activities	(17,942		)	(23,375		)	(13,796		)	(10,299		)
Investing activities
Purchases of property and equipment	(654		)	(174		)	(233		)	(221		)
Proceeds from sale of equipment	19			72			16			—
Net cash used in investing activities	(635		)	(102		)	(217		)	(221		)
Financing activities
Proceeds from equity offerings, net	—			2,920
Proceeds from issuance of common stock, net	52,194			52,538			440			—
Payment of deferred financing costs	—			(127		)
Proceeds from long-term debt	—			592
Payments on finance lease							(45		)	—
Proceeds from equity offerings, net of issuance costs							—			14,026
Repayment of long-term debt	(1,377		)	(535		)	—			(841		)
Proceeds from exercise of stock options	21			—			—			12
Proceeds from the issuance of common stock under ESPP	48			31
Net cash provided by financing activities	50,886			55,419			395			13,197
Net increase in cash and cash equivalents	$	32,309		$	31,942
Net (decrease) increase in cash, cash equivalents and restricted cash							$	(13,618	)	$	2,677
Cash, cash equivalents and restricted cash at beginning of period	26,677			12,589			40,758			26,677
Cash, cash equivalents and restricted cash at end of period	$	58,986		$	44,531		$	27,140		$	29,354
Supplemental cash flow information
Non-cash financing activities and supplemental cash flow information
Right-of-use asset obtained in exchange for lease liabilities							$	5,931		$	1,686
Cash paid in connection with operating lease liabilities							$	394		$	406
Cash paid for interest	$	577		$	508		$	261		$	289
Property and equipment included in accounts payable and accrued expenses	$	127		$	—
Reclassification of warrants to additional paid-in capital	$	—		$	190

See accompanying notes to unaudited condensed consolidated financial statements.

Genocea Biosciences, Inc.

Notes to Condensed Consolidated Financial Statements

(unaudited)

1. Organization and operations

The Company

Genocea Biosciences, Inc. (the “Company”) is a biopharmaceutical company that was incorporated in Delaware on August 16, 2006 and has a principal place of business in Cambridge, Massachusetts. The Company seeks to discover and develop novel cancer immunotherapies using its ATLAS^TM proprietary discovery platform. The ATLAS platform profiles each patient's CD4⁺ and CD8⁺ T cell immune responses to every potential target or ~~"antigen"~~“antigen” in that patient's tumor. ~~Genocea~~The Company believes that this approach optimizes antigen selection for immunotherapies such as cancer vaccines and cellular ~~therapies, because it identifies antigens to which a patient’s T cells already mount anti-tumor responses. The~~therapies. Consequently, the Company believes that ATLAS could lead to more immunogenic and efficacious cancer immunotherapies.

The Company’s most advanced program is GEN-009, a personalized neoantigen cancer vaccine, for which it is conducting a Phase 1/2a clinical trial. The GEN-009 program uses ATLAS to identify neoantigens, or immunogenic tumor mutations unique to each patient, for inclusion in each patient's GEN-009 vaccine. The Company is also advancing GEN-011, a neoantigen-specific adoptive T cell therapy program ~~as well as GEN-010, a follow-on neoantigen vaccine program.~~that also relies on ATLAS, and expects to file an IND in the second quarter of 2020.

The Company is devoting substantially all of its efforts to product research and development, initial market development, and raising capital. The Company has not generated any product revenue related to its primary business purpose to date and is subject to a number of risks ~~similar~~and uncertainties common to those of other early clinical stage companies, including dependence on key individuals, competition from other companies, the need and related uncertainty associated to the development of commercially viable products, and the need to obtain adequate additional financing to fund the development of its product candidates. The Company is also subject to a number of risks similar to other companies in the ~~life sciences~~biotech and pharmaceutical industry, including, but not limited to, the risks associated with the uncertainty of success of its preclinical and clinical ~~trials,~~trials; the challenges associated with gaining regulatory approval of product candidates; the risks associated with commercializing pharmaceutical products, if approved for marketing and sale; the potential for development by third parties of new technological innovations that may compete with the Company’s products; the dependence on ~~third parties,~~key personnel; the challenges of protecting proprietary technology; the need to ~~obtain additional financing, dependence on key individuals, regulatory approval~~comply with government regulations; the high cost of ~~products, uncertainty of market acceptance of products, competition from companies with greater financial, technological and other resources,~~drug development; compliance with government regulations, ~~protection~~competition from other companies; the uncertainty of ~~proprietary technology,~~being able to secure additional capital when needed to fund operations; and ~~product liability. The Company has historical losses from~~the challenges and uncertainty associated with the recent outbreak of the coronavirus, or referred to as COVID-19, that have arisen in the global economy, that could adversely impact the Company's operations, supply chain, preclinical development work, clinical trials and ~~anticipates that it will continue~~ability to ~~incur significant operating losses for the foreseeable future as it continues to develop its product candidates.~~raise capital.

Effective May 22, 2019, the Company effected a reverse stock split of its issued and outstanding common stock, par value $0.001, at a ratio of one-for-eight, and decreased the number of authorized shares of common stock from 250,000,000 shares to 85,000,000 shares. The share and per share information presented in these financial statements and related notes have been retroactively adjusted to reflect the one-for-eight reverse stock split.

~~Operating Capital Requirements~~

~~Under~~ Accounting Standards Update ~~("ASU"~~(“ASU”), 2014-15, Presentation of Financial Statements-Going Concern (Subtopic 205-40), also referred to as Accounting Standards Codification ~~("ASC"~~(“ASC”) 205-40 (“ASC 205-40”), requires the Company ~~has the responsibility~~ to evaluate whether conditions and/or events raise substantial doubt about its ability to meet its future financial obligations as they become due within one year after the ~~date that the~~ financial statements are issued. As of March 31, 2020, the Company had an accumulated deficit of $343.8 million and anticipates that it will continue to incur significant operating losses for the foreseeable future as it continues to develop its product candidates. Until such time, if ever, as the Company can generate substantial product revenue and achieve profitability, the Company expects to finance its cash needs through a combination of equity offerings, strategic transactions, and other sources of funding. If the Company is unable to raise additional funds when needed, the Company may be required ~~by ASC 205-40, this evaluation shall initially not take into consideration the potential mitigating effects~~to implement further cost reduction strategies, including ceasing development of plans that have not been fully implemented as of the date the financial statements are issued. Management has assessed the Company’s ability to continue as a going concern in accordance with the requirement of ASC 205-40.GEN-009, GEN-011, or other corporate programs and activities.

As reflected in the ~~condensed~~ consolidated financial statements, the Company had available cash and cash equivalents of ~~$58.7~~$26.5 million at ~~June 30, 2019. The~~March 31, 2020. In addition, the Company ~~believes that its~~had cash used in operating activities of $13.8 million for the three months ended March 31, 2020. These factors, combined with the Company’s forecast of cash ~~equivalents and investments will~~required to fund ~~its~~ operations ~~into~~for a period of at least one year from the ~~first quarter~~date of ~~2021.~~

~~The Company plans~~issuance of these consolidated financial statements, raise substantial doubt about the Company’s ability to continue to fund its operations through public or private equity offerings, strategic transactions, proceeds from sales of its common stock under its at-the-market equity offering program, or by other means. However, adequate additional financing may not be available to the Company on acceptable terms, or at all. If the Company is unable to raise capital when needed, or on attractive terms, it may be forced to implement cost reduction strategies, including ceasing development of GEN-009, GEN-011, and other corporate programs and activities.as a going concern.

The accompanying consolidated financial statements have been prepared on a going concern basis, which contemplates the realization of assets and satisfaction of liabilities in the ordinary course of business. The consolidated financial statements do not include any adjustments relating to the recoverability and classification of recorded asset amounts or the amounts and classification of liabilities that might result from the outcome of this uncertainty.

2. Summary of significant accounting policies

~~Basis~~The following is a summary of ~~presentation~~

Insignificant accounting policies followed in the ~~opinion~~preparation of ~~management, the accompanying unaudited~~these condensed consolidated financial statements include all adjustments, consisting of normal recurring accruals necessary for a fair presentation of the Company’s financial statements for interim periods in accordance with accounting principles generally accepted in the United States (U.S. GAAP).

~~We operate as one operating segment, which is discovering, researching and developing novel cancer immunotherapies.~~statements.

The information included in this Quarterly Report on Form 10-Q should be read in conjunction with ~~our~~the Company's audited consolidated financial statements and the accompanying notes included in ~~our~~the Company's Annual Report on Form 10-K for the year ended December 31, ~~2018~~2019 (“~~2018~~2019 Form 10-K”). ~~Our~~The Company's accounting policies are described in the “Notes to Consolidated Financial Statements” in ~~our 2018~~the Company's 2019 Form 10-K and updated, as necessary, in ~~our~~the Company's Quarterly Reports on Form 10-Q. The December 31, ~~2018~~2019 condensed consolidated balance sheet data presented for comparative purposes ~~was~~were derived from ~~our~~the Company's audited financial statements but ~~does~~do not include all disclosures required by U.S. GAAP. The results of operations for the three ~~and six~~ months ended ~~June 30, 2019~~March 31, 2020 are not necessarily indicative of the operating results for the full year or for any other subsequent interim period.

Basis of presentation

The accompanying unaudited condensed consolidated financial statements include those accounts of the Company and a wholly owned subsidiary after elimination of all intercompany accounts and transactions. The Company operates as one segment, which is discovering, researching, developing and commercializing novel cancer immunotherapies.

Use of ~~Estimates~~estimates

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. On an ongoing basis, the Company’s management evaluates its estimates, which include, but are not limited to, estimates related to clinical trial accruals, estimates related to prepaid and accrued research and development expenses, stock-based compensation expense, and warrants to purchase redeemable securities. The Company bases its estimates on historical experience and other market-specific or other relevant assumptions that it believes to be reasonable under the circumstances. Actual results may differ from those estimates or assumptions.

~~Summary of~~ Significant ~~Accounting Policies~~accounting policies

There were no changes to significant accounting policies during the ~~six~~three months ended ~~June 30, 2019,~~March 31, 2020, as compared to the those ~~identified~~disclosed in the ~~2018~~2019 Form ~~10-K, except for~~10-K.

New Accounting Pronouncements

The following new accounting pronouncements were adopted by the ~~Company's adoption of ASC Topic 842,~~ ~~Leases~~ Company on January 1, ~~2019. The following is the Company's new accounting policy for leases.~~2020:

~~Leases~~In 2016, the Financial Accounting Standards Board (“FASB”) issued ASU 2016-13, Financial Instruments-Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments (“ASU 2016-13”), which amends the impairment model by requiring entities to use a forward-looking approach based on expected losses to estimate credit losses on certain types of financial instruments, including trade receivables and available-for-sale debt securities. The Company early adopted the standard on January 1, 2020. Based on the composition of the Company's investment portfolio, which includes only money market funds, and the insignificance of the Company's other financial assets, current market conditions, and historical credit loss activity, the adoption of this standard did not have a material impact on the Company's consolidated financial statements and related disclosures.

AtIn 2018, the ~~inception~~FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework – Changes to the Disclosure Requirements for Fair Value Measurement (“ASU 2018-13”). The new standard requires public entities to disclose certain new information and modifies some disclosure requirements. The Company adopted the standard on the required effective date of January 1, 2020. This standard did not have a material impact on the ~~contract,~~Company's disclosures.

In 2018, the ~~Company determines if an~~FASB issued ASU 2018-15, Intangibles-Goodwill and Other-Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract (“ASU 2018-15”). ASU 2018-15 requires a customer in a cloud computing arrangement that is a ~~lease~~service contract to follow the internal-use software guidance in Accounting Standards Codification 350-40 to determine which implementation costs to defer and ~~has~~recognize as an asset. The Company adopted the standard on the required effective date of January 1, 2020. This standard did not have a lease term greater than 12 months. Leases that are concluded to be operating leases are included in operating lease right-of-use (“ROU”) assets and operating lease liabilities in the consolidated balance sheets. Leases that are concluded to be finance leases are included in property and equipment and other current liabilities in the consolidated balance sheets.

~~ROU assets represent~~material impact on the Company's ~~right to use an underlying asset for the lease term~~consolidated financial statements and lease liabilities represent the Company's obligation to make lease payments arising from the lease. Operating lease ROU assets and liabilities are recognized at the lease commencement date based on the present value of lease payments over the lease term. As most of the Company's leases do not provide an implicit rate, the Company uses an estimate of its incremental borrowing rate based on the information available at the lease commencement date in determining the present value of lease payments. The Company uses the implicit rate when readily determinable. The operating lease ROU asset is reduced by deferred lease payments and unamortized lease incentives. The Company's lease terms may include options to extend or terminate the lease when it is reasonably certain that the Company will exercise that option. Lease expense for lease payments is recognized on a straight-line basis over the lease term. The Company has lease agreements with lease and non-lease components, which are generally accounted for separately. The non-lease components generally consist of common area maintenance that is expensed as incurred.related disclosures.

The following new accounting pronouncements have been issued but are not yet effective:

In 2019, the FASB issued ASU 2019-12, Income Taxes (Topic 740): Simplifying the Accounting for Income Taxes ("ASU 2019-12"). ASU 2019-12 simplifies the accounting for income taxes and will be effective beginning after December 15, 2020. The Company is currently evaluating the impact of ASU 2019-12 in the consolidated financial statements, including accounting policies, processes, and systems.

~~Recently adopted~~Other accounting standards



~~Standard~~	~~Description~~	~~Effect on the financial statements~~
~~ASU No. 2016-02,~~ ~~Leases (Topic 842)~~	~~In February 2016, the FASB established ASC Topic 842,~~ ~~Leases~~, (ASC 842) by issuing ASU No. 2016-02, which requires lessees to recognize leases on-balance sheet and disclose key information about leasing arrangements. Topic 842 was subsequently amended by ASU No. 2018-01, Land Easement Practical Expedient for Transition to Topic 842; ASU No. 2018-10, Codification Improvements to Topic 842, Leases; and ASU No. 2018-11, Targeted Improvements. The new standard establishes a right-of-use model ("ROU") that requires a lessee to recognize a ROU asset and lease liability on the balance sheet for all leases with a term longer than 12 months. Leases are classified as finance or operating, with classification affecting the pattern and classification of expense recognition in the income statement. ~~The Company adopted ASC 842 effective January 1, 2019.~~	The adoption of ASC 842 resulted in the Company recognizing ROU assets and related operating lease liabilities of $1.7 million and $1.8 million, respectively, in our condensed consolidated balance sheet as of January 1, 2019. The Company used the modified retrospective method of adoption, with January 1, 2019 as the effective date of initial application. The Company elected the short-term lease recognition exemption for all leases that qualify. The Company elected the package of practical expedients for leases that commenced prior to January 1, 2019, allowing it not to reassess (i) whether any expired or existing contracts contain leases, (ii) the lease classification for any expired or existing leases and (iii) the initial indirect costs for any existing leases.
~~ASU No. 2018-07,~~ ~~Compensation-Stock Compensation (Topic 718): Improvements to Nonemployee Share-Based Payment Accounting~~	~~In June 2018, the FASB issued ASU No. 2018-07,~~ ~~Compensation-Stock Compensation (Topic 718): Improvements to Nonemployee Share-Based Payment Accounting.~~ The new standard largely aligns the accounting for share-based payment awards issued to employees and nonemployees by expanding the scope of ASC 718 to apply to nonemployee share-based transactions, as long as the transaction is not effectively a form of financing. ~~The Company adopted ASU No. 2018-07 effective January 1, 2019.~~	~~The adoption of ASU No. 2018-07 did not have a material impact on the Company's condensed consolidated financial statements.~~

~~Recently~~ that have been issued ~~accounting standards~~



~~Standard~~	~~Description~~	~~Effect on the financial statements~~
~~ASU 2016-13,~~ ~~Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments~~	~~In June 2016, the FASB issued ASU 2016-13,~~ ~~Financial Instruments-Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments,~~ which amends the impairment model by requiring entities to use a forward-looking approach based on expected losses to estimate credit losses on certain types of financial instruments, including trade receivables and available-for-sale debt securities. ~~The new guidance will be effective for the Company beginning in the first quarter of 2020, with early adoption permitted.~~	~~The Company is currently evaluating the potential impact that this standard may have on its consolidated financial statements.~~
~~ASU 2018-13,~~ ~~Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement~~	~~In August 2018, the FASB issued ASU 2018-13,~~ ~~Fair Value Measurement (Topic 820): Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement~~ ~~which requires public entities to disclose certain new information and modifies some disclosure requirements.~~ ~~The new guidance will be effective for fiscal years beginning after December 15, 2019 and for interim periods within those fiscal years.~~	~~The Company is currently evaluating the potential impact that this standard may have on its consolidated financial statements.~~
~~ASU 2018-15,~~ ~~Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract.~~	~~In August 2018, the FASB issued ASU 2018-15,~~ ~~Intangibles - Goodwill and Other - Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract.~~ ASU 2018-15 requires a customer in a cloud computing arrangement that is a service contract to follow the internal-use software guidance in Accounting Standards Codification 350-40 to determine which implementation costs to defer and recognize as an asset. ~~The new guidance will be effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2019.~~	~~The Company is currently evaluating the potential impact that this standard may have on its consolidated financial statements.~~

or proposed by the FASB or other standards-setting bodies that do not require adoption until a future date are not expected to have a material impact on the Company’s consolidated financial statements upon adoption.

3. Fair value of financial instruments

The Company has certain financial assets and liabilities recorded at fair value which have been classified as Level 1, 2 or 3 within the fair value hierarchy as described in the accounting standards for fair value measurements.

Level ~~1 -~~ 1—Fair values are determined by utilizing quoted prices (unadjusted) in active markets for identical assets or liabilities that the Company has the ability to access;

Level ~~2 -~~ 2—Fair values are determined by utilizing quoted prices for similar assets and liabilities in active markets or other market observable inputs such as interest rates, yield curves and foreign currency spot rates; and

Level ~~3 -~~ 3—Prices or valuations that require inputs that are both significant to the fair value measurement and unobservable.

The Company's financial assets consist of cash equivalents and the Company's financial liabilities consist of a warrant liability.

The fair value of the Company’s cash equivalents is determined using quoted prices in active markets. ~~Our~~The Company's cash equivalents consist of money market ~~funds. The Company’s cash equivalents have been~~funds that are classified as Level 1.

The fair value of the Company’s warrant liability is determined using a Monte Carlo simulation. See Note 7.8. Warrants~~. The~~ for assumptions used and methodologies utilized in calculating the estimated fair value of the warrants represent the Company’s best estimates and include probabilities of settlement scenarios, future changes in the Company’s stock price, risk-free interest rates, volatility and probability of the Company being acquired. The estimates are based, in part, on subjective assumptions and could differ materially in the future.value. The Company’s warrant liability ~~has been~~is classified as Level 3.

The following table sets forth the Company's assets and liabilities that are measured at fair value on a recurring basis as of March 31, 2020 and December 31, 2019 (in thousands):


			Quoted prices in active markets		Significant other observable inputs		Significant unobservable inputs				Quoted prices in active markets		Significant other observable inputs		Significant unobservable inputs
	Total		(Level 1)		(Level 2)		(Level 3)		Total		(Level 1)		(Level 2)		(Level 3)
June 30, 2019
March 31, 2020
Assets:
Cash equivalents	$	19,802	$	19,802	$	—	$	—	$	25,985	$	25,985	$	—	$	—
Total assets	$	19,802	$	19,802	$	—	$	—	$	25,985	$	25,985	$	—	$	—

Liabilities:
Warrant liability	$	5,389	$	—	$	—	$	5,389	$	1,705	$	—	$	—	$	1,705
Total liabilities	$	5,389	$	—	$	—	$	5,389	$	1,705	$	—	$	—	$	1,705

December 31, 2018
December 31, 2019
Assets:
Cash equivalents	$	24,651	$	24,651	$	—	$	—	$	39,971	$	39,971	$	—	$	—
Total assets	$	24,651	$	24,651	$	—	$	—	$	39,971	$	39,971	$	—	$	—

Liabilities:
Warrant liability	$	3,472	$	—	$	—	$	3,472	$	2,486	$	—	$	—	$	2,486
Total liabilities	$	3,472	$	—	$	—	$	3,472	$	2,486	$	—	$	—	$	2,486

The following table reflects the change in the Company’s Level 3 warrant liability ~~from December 31, 2018 through June 30, 2019:~~(in thousands):

Warrant Liability
Balance at December 31, 2018 $ 3,472
Change in fair value 1,917
Balance at June 30, 2019 $ 5,389



	Warrant Liability
Balance at December 31, 2019	$	2,486
Change in fair value	(781		)
Balance at March 31, 2020	$	1,705

4. Accrued expenses and other current liabilities

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


	June 30,		December 31,		March 31,		December 31,
	2019		2018		2020		2019
Research and development	$	1,462	$	759
Payroll and employee-related	1,491		2,147
Research and development costs					$	2,507	$	1,607
Payroll and employee-related costs					730		2,245
Other current liabilities	2,097		910		840		759
Total	$	5,050	$	3,816	$	4,077	$	4,611

5. Commitments and contingencies

Operating leases

As of March 31, 2020, the Company has leases for three floors of lab and office space in a multi-tenant building in Cambridge, Massachusetts.

In July 2019, the Company exercised an option for additional office and lab space from March 2020 through February 2025. The Company's right to use and control the space began in March 2020. As a result of the Company's right to use and control the space, the Company recognized an increase in the right of use (“ROU”) assets of $5.9 million and associated lease liabilities of $5.8 million in March 2020. The Company has the option to extend the lease term for an additional five years, which is not included in the Company's ROU assets and associated lease liabilities as of March 31, 2020.

In May 2019, the Company entered into a lease extension for office and lab space through February 2025. As a result of the lease term extension, the Company recognized an increase in the ROU assets of $5.4 million and associated lease liabilities of $5.3 million. The associated lease obligation for the extension is included in the Company’s ROU assets and associated lease liabilities as of March 31, 2020. The Company has the option to extend the lease terms for an additional five years, which is not included in the Company's ROU assets and associated lease liabilities as of March 31, 2020.

For the three months ended March 31, 2020 and 2019 lease expense, net of sublease income, was $0.5 million and $0.4 million, respectively.

The weighted average remaining lease term and weighted average discount rate of the Company's operating leases are as follows:

Finance lease

In December 2019, the Company entered into an agreement to lease lab equipment for a term of 15 months. The Company determined that the agreement qualifies as a finance lease based on the criteria that the Company holds the option to purchase the asset and is reasonably certain to exercise at the end of the lease term. The ROU asset and lease liability were calculated using an incremental borrowing rate of 7.95%. Lease payments on this lease began in January 2020.

The following table summarizes the presentation in the Company's consolidated balance sheets:



Leases (in thousands)	Classification	March 31, 2020		December 31, 2019
Assets
Operating	Lease ROU asset	$	11,663	$	6,156
Finance	Lease ROU asset	119		150
Total lease assets		$	11,782	$	6,306
Liabilities
Current
Operating	Lease liabilities	$	1,921	$	990
Finance	Lease liabilities	107		127
Non-current
Operating	Lease liabilities, net of current portion	9,994		5,373
Finance	Lease liabilities, net of current portion	—		22
Total lease liabilities		$	12,022	$	6,512

The minimum lease payments related to the Company's operating and finance leases in accordance with ASC 842 as of March 31, 2020 were as follows (in thousands):



	Operating leases			Finance lease			Total
2020	$	2,110		$	89		$	2,199
2021	2,871			23			2,894
2022	2,943			—			2,943
2023	3,017			—			3,017
2024 and thereafter	3,609			—			3,609
Total lease payments	$	14,550		$	112		$	14,662
Less imputed interest	(2,635		)	(5		)	(2,640		)
Total	$	11,915		$	107		$	12,022

At March 31, 2020 and December 31, 2019, the Company has an outstanding letter of credit of $0.6 million, with a financial institution related to a security deposit for the office and lab space lease, which is secured by cash on deposit and expires on February 28, 2025.

Contractual obligations

The Company has entered into certain agreements with various contract research organizations (“CROs”) and contract manufacturing organizations (“CMOs”), which generally include cancellation clauses.

Harvard University License Agreement

The Company has an exclusive license agreement with Harvard University (“Harvard”), granting the Company an exclusive, worldwide, royalty-bearing, sublicensable license to three patent families, to develop, make, have made, use, market, offer for sale, sell, have sold and import licensed products and to perform licensed services related to the ATLAS discovery platform. The Company is also obligated to pay Harvard milestone payments up to $1.6 million in the aggregate upon the achievement of certain development and regulatory milestones. As of March 31, 2020, the Company has paid $0.3 million in aggregate milestone payments. The Company is obligated under this license agreement to use commercially reasonable efforts to develop, market and sell licensed products in compliance with an agreed upon development plan. In addition, the Company is obligated to achieve specified development milestones and in the event the Company is unable to meet its development milestones for any type of product or service, absent any reasonable proposed extension or amendment thereof, Harvard has the right, depending on the type of product or service, to terminate this agreement with respect to such products or to convert the license to a non-exclusive, non-sublicensable license with respect to such products and services.

Upon commercialization of our products covered by the licensed patent rights or discovered using the licensed methods, the Company is obligated to pay Harvard royalties on the net sales of such products and services sold by the Company, the Company's

affiliates, and the Company's sublicensees. This royalty varies depending on the type of product or service but is in the low single digits. The sales-based royalty due by the Company’s sublicensees is the greater of the applicable royalty rate or a percentage in the high single digits or the low double digits of the royalties the Company receives from such sublicensee, depending on the type of product. Based on the type of commercialized product or service, royalties are payable until the expiration of the last-to-expire valid claim under the licensed patent rights or for a period of 10 years from first commercial sale of such product or service. The royalties payable to Harvard are subject to reduction, capped at a specified percentage, for any third-party payments required to be made. In addition to the royalty payments, if the Company receives any additional revenue (cash or non-cash) under any sublicense, the Company must pay Harvard a percentage of such revenue, excluding certain categories of payments, varying from the low single digits to up to the low double digits depending on the scope of the license that includes the sublicense.

This license agreement with Harvard will expire on a product-by-product or service-by-service and country-by-country basis until the expiration of the last-to-expire valid claim under the licensed patent rights. The Company may terminate the agreement at any time by giving Harvard advance written notice. Harvard may also terminate the agreement in the event of a material breach by the Company that remains uncured; in the event of our insolvency, bankruptcy, or similar circumstances; or if the Company challenges the validity of any patents licensed to us.

Oncovir License and Supply Agreement

In January 2018, the Company entered into a License and Supply Agreement with Oncovir, Inc. (“Oncovir”). The agreement provides the terms and conditions under which Oncovir will manufacture and supply an immunomodulator and vaccine adjuvant, Hiltonol® (poly-ICLC) (“Hiltonol”), to the Company for use in connection with the research, development, use, sale, manufacture, commercialization and marketing of products combining Hiltonol with the Company's technology (the “Combination Product”). Hiltonol is the adjuvant component of GEN-009, which will consist of synthetic long peptides or neoantigens identified using the Company's proprietary ATLAS platform, formulated with Hiltonol.

Oncovir granted the Company a non-exclusive, assignable, royalty-bearing worldwide license, with the right to grant sublicenses through one tier, to certain of Oncovir’s intellectual property in connection with the research, development, or commercialization of Combination Products, including the use of Hiltonol, but not the use of Hiltonol for manufacturing or the use or sale of Hiltonol alone. The license will become perpetual, fully paid-up, and royalty-free on the later of January 25, 2028 or the date on which the last valid claim of any patent licensed to the Company under the agreement expires.

Under this agreement, the Company is obligated to pay Oncovir low to mid six figure milestone payments upon the achievement of certain clinical trial milestones for each Combination Product and the first marketing approval for each Combination Product in certain territories, as well as tiered royalties in the low-single digits on a product-by-product basis based on the net sales of Combination Products.

The Company may terminate the agreement upon a decision to discontinue the development of the Combination Product or upon a determination by the Company or an applicable regulatory authority that Hiltonol or a Combination Product is not clinically safe or effective. The agreement may also be terminated by either party due to a material uncured breach by the other party, or due to the other party’s bankruptcy, insolvency, or dissolution.

6. Long-term debt

In Q2April 2018, the Company entered into an amended and restated loan and security agreement ~~(the~~with Hercules Capital, Inc.(“Hercules”), which was subsequently amended in November 2019 (as amended, the “2018 Term Loan”) ~~with Hercules Capital, Inc. (“Hercules”), which provided~~. The 2018 Term Loan provides a $14.0 million term loan. The 2018 Term Loan ~~will mature~~matures on May 1, 2021 and accrues interest at a floating rate per annum equal to the greater of (i) ~~7.75%~~8.00%, or (ii) the sum of ~~2.75%~~3.00% plus the prime rate. The 2018 Loan Agreement ~~provided~~provides for interest-only payments until ~~June~~January 1, ~~2019. Since the Company met certain performance milestones, interest-only payments have been extended until June 1, 2020.~~2021. Thereafter, payments will include equal installments of principal and interest through maturity. The 2018 Term Loan may be prepaid subject to a prepayment charge. The Company is obligated to pay an additional end of term charge of ~~6.7%.~~

$1.0 million at maturity.

The 2018 Term Loan is secured by a lien on substantially all assets of the Company, other than intellectual property. Hercules has a perfected first-priority security interest in certain cash, cash equivalents and investment accounts. The 2018 Term Loan contains non-financial covenants, representations and a (“Material Adverse ~~Effect”) provision.~~Effect provision, as defined herein. There are no financial covenants. A ~~Material~~“Material Adverse ~~Effect~~Effect” means a material adverse effect upon: (i) the business, operations, properties, assets or condition (financial or otherwise) of the Company; or (ii) the ability of the Company to perform the secured obligations in accordance with the terms of the loan documents, or the ability of agent or lender to enforce any of its rights or remedies with respect to the secured obligations; or (iii) the collateral or agent’s liens on the collateral or the priority of such liens. Any event that has a Material Adverse Effect or would reasonably be expected to have a Material Adverse Effect is an event of default under the Loan Agreement and repayment of amounts

due under the Loan Agreement may be accelerated by Hercules under the same terms as an event of default. As of ~~June 30, 2019,~~March 31, 2020, the Company was in compliance with all covenants of the 2018 Term Loan. The 2018 Term Loan is automatically redeemable upon a change in control. The Company believes acceleration of the repayment of amounts outstanding under the loan is remote, and therefore, the debt balance is classified according to the contractual payment terms at ~~June 30, 2019.~~March 31, 2020.

In connection with ~~a previously issued term loan in 2014 and~~ the 2018 Term Loan, the Company issued common stock warrants to Hercules (the ~~“First Warrant and Second~~“Hercules Warrant”~~, respectively)~~). See Note 7.8. Warrants.

As of ~~June 30, 2019~~March 31, 2020 and December 31, ~~2018,~~2019, the Company had outstanding borrowings of ~~$13.7~~$13.5 million and ~~$14.8~~$13.4 million, respectively. Interest expense was $0.4 million for each of the three months ended ~~June 30, 2019~~March 31, 2020 and ~~2018 and $0.9 million and $0.8 million for the six months ended June 30, 2019 and 2018, respectively. At June 30, 2019, the 2018 Term Loan bears an effective interest rate of 11.4%.~~2019.

Future principal payments, including the End of Term Charges, are as follows (in thousands):

June 30, 2019
2019 $ 542
2020 7,399
2021 6,462
Total $ 14,403

~~The Company's balance sheet classification has been updated to reflect the extension of interest only payments.~~



	March 31, 2020
2020	$	—
2021	13,960
Total	$	13,960

6.7. Stockholders' equity

~~As of June 30,~~Agreement with Lincoln Park Capital

In October 2019, the Company entered into a purchase agreement with Lincoln Park Capital (“LPC”) pursuant to which LPC purchased $2.5 million of shares of the Company's common stock at a purchase price of $2.587 per share. In addition, for a period of thirty months, the Company has ~~authorized 85,000,000~~the right, at its sole discretion, to sell up to an additional $27.5 million of the Company's common stock based on prevailing market prices of its common stock at the time of each sale. In consideration for entering into the purchase agreement, the Company issued 289,966 shares of its common stock to LPC as a commitment fee. The purchase agreement limits the Company's sales of shares of common stock ~~at $0.001 par value per share and 25,000,000 shares of preferred stock at $0.001 par value per share. As of June 30, 2019, 26,149,689~~to LPC to 5,227,323 shares of common stock, ~~and 1,635 shares~~representing 19.99% of ~~preferred stock were issued and outstanding. As of December 31, 2018, 10,846,397~~the shares of common stock ~~were issued and~~ outstanding ~~and 1,635~~on the date of the purchase agreement. The purchase agreement also prohibits the Company from directing LPC to purchase any shares of ~~preferred~~common stock ~~were issued~~if those shares, when aggregated with all other shares of the Company's common stock then beneficially owned by LPC and ~~outstanding.~~its affiliates, would result in LPC and its affiliates having beneficial ownership, at any single point in time, of more than 9.99% of the then total outstanding shares of the Company's common stock.

In January 2020, the Company sold 186,986 shares of common stock to LPC, and received net proceeds of approximately $0.4 million.

2019 Public Offering

OnIn June ~~21,~~ 2019, the Company entered into an underwriting agreement relating to the ~~underwritten~~ public offering of 10,500,000 shares of the Company’s common stock, ~~par value $0.001 per share,~~ at a price ~~to the public~~ of $3.50 per share, for gross proceeds of approximately $36.8 million (the “2019 Public Offering”).

~~Under the terms of the underwriting agreement for the 2019 Public Offering, the~~ The Company also granted the underwriters an option to purchase up to an additional 1,575,000 shares of common stock (“Overallotment Option”). On June 26, 2019, the underwriters exercised this option in full. The Company received approximately $5.5 million in gross proceeds from the underwriter’s exercise of the Overallotment Option.

In connection with the 2019 Public Offering, inclusive of the Overallotment Option, the Company ~~incurred approximately $3.9 million of offering-related expenses, resulting in total~~received net proceeds of $38.4 million.

Private Placement

In February 2019, the Company completed a private placement financing transaction (the “Private Placement”). The Company issued 3,199,998 shares ~~(the “Shares”)~~ of common stock, prefunded warrants (the “Pre-Funded Warrants”) to purchase 531,250 shares of common stock (the “Pre-Funded Warrant Shares”), and warrants (the “Private Placement Warrants”) to purchase up to 932,812

shares of common stock (the “Warrant Shares”). The ~~Shares,~~shares, Pre-Funded Warrants and Private Placement Warrants (collectively, the “Units”) were sold at a purchase price of $4.02 per Unit. The Company received net cash proceeds of approximately $13.8 million for the purchase of the ~~Shares,~~shares, Pre-Funded Warrant Shares and Warrant Shares. See Note 7.8. Warrants.

The Company had the option to issue additional shares of common stock in a second closing (the “Second Closing”) for gross proceeds of up to $24.2 million. The occurrence of the Second Closing was conditioned on top-line results from Part A of ~~our~~the Company's Phase 1/2a clinical trial for GEN-009 and a decision by ~~our~~the Company's board of directors to proceed with the Second

Closing. In June 2019, the Company announced top-line results from this trial but elected not to proceed with the Second Closing. In lieu of the Second Closing, the Company proceeded with the 2019 Public Offering.

~~2018 Public Offering~~

In January 2018, the Company entered into two underwriting agreements, the first relating to the underwritten public offering of 6,670,625 shares of the Company’s common stock, par value $0.001 per share, and accompanying warrants to purchase up to 3,335,313 shares of common stock (“2018 Public Offering Warrants”), at a combined price of $8.00 per share, for gross proceeds of approximately $53.4 million (the “2018 Common Stock Offering”) and the second relating to the underwritten public offering of 1,635 shares of the Company’s Series A convertible preferred stock, par value $0.001 per share, which are convertible into 204,375 shares of common stock, and accompanying warrants to purchase up to 102,188 shares of common stock for gross proceeds of approximately $1.6 million (the “Preferred Stock Offering,” and together with the 2018 Common Stock Offering, the “January 2018 Financing”). The Company also granted the underwriters an Overallotment Option ("Overallotment Option") to purchase up to an additional 1,000,594 shares of common stock and/or additional warrants to purchase up to 500,297 shares of common stock. The underwriters exercised their Overallotment Option and acquired additional warrants to purchase up to 299,475 shares of common stock.

~~Preferred Stock~~

Each share of preferred stock is convertible at any time at the option of the holder, provided that the holder will be prohibited from converting the preferred stock into shares of common stock if, as a result of such conversion, the holder, together with its affiliates, would own more than 9.99% of the total number of shares of common stock then issued and outstanding. Each share of preferred stock is convertible into 125 shares of common stock, subject to certain adjustments upon stock dividends and stock splits.

~~The preferred stock ranks~~ ~~pari passu~~ on an as-converted to common stock basis with the common stock as to distributions of assets upon the Company’s liquidation, dissolution or winding up, whether voluntarily or involuntarily, or a “Fundamental Transaction,” as defined in the Certificate of Designation. Shares of preferred stock have no voting rights, except as required by law and except that the consent of the holders of a majority of the outstanding preferred stock is required to amend the terms of the preferred stock. The holders of preferred stock shall be entitled to receive dividends in the same form as dividends actually paid on shares of common stock when, as and if such dividends are declared and paid on shares of the common stock, on an as-if-converted-to-common stock basis.

~~The Company determined that the preferred stock should be equity classified in accordance with ASC 480,~~ ~~Distinguishing Liabilities from Equity~~ (“ASC 480”) for the periods ended June 30, 2019 and December 31, 2018, respectively. For the six months ended June 30, 2018, the Company recorded $0.3 million in additional paid-in capital as a result of the preferred stock’s beneficial conversion feature.

~~Issuance Costs~~

In connection with the January 2018 Financing, the Company incurred approximately $4.0 million of issuance costs. The Company allocated approximately $2.6 million of the issuance costs to the common and preferred stock, and recorded these amounts within additional paid-in capital, and approximately $1.4 million of the issuance costs to the 2018 Public Offering Warrants. As the 2018 Public Offering Warrants were classified as liabilities, the Company immediately expensed the issuance costs allocated to the 2018 Public Offering Warrants in the three months ended March 31, 2018.

~~Warrants~~

~~See~~ ~~Note 7. Warrants.~~

~~Hercules~~

~~In connection with the 2018 Loan Agreement with Hercules, see~~ ~~Note 5.Long-term debt~~, the Company also entered into an amendment to the November 2014 equity rights letter agreement (the “Amended Equity Rights Letter Agreement”). Hercules has the right to participate in any one or more subsequent private placement equity financings of up to $2.0 million on the same terms and conditions as purchases by the other investors in each subsequent equity financing. The Amended Equity Rights Letter Agreement will terminate upon the earlier of (1) such time when Hercules has purchased $2.0 million of subsequent equity financing securities in the aggregate, and (2) the later of (a) the repayment of all indebtedness under the Loan Agreement, or (b) the expiration or termination of the exercise period for the Second Warrant. See ~~Note 7. Warrants~~.

At-the-market equity offering program

In 2015, the Company entered into an agreement, as amended, with Cowen and Company, LLC to establish an at-the-market equity offering program (“ATM”) pursuant to which it was able to offer and sell ~~up to $50 million~~shares of its common stock at prevailing market prices from time to time. Through ~~June 30, 2019,~~March 31, 2020, the Company has sold an aggregate of ~~approximately 0.5 million~~463,887 shares under the ATM and received approximately $4.0 million in net ~~proceeds after deducting commissions.~~proceeds.

7.8. Warrants

As of ~~June 30, 2019,~~March 31, 2020, the Company had the following potentially issuable shares of common stock related to unexercised warrants outstanding:


	Shares	Exercise price		Expiration date	Classification	Shares	Exercise price		Expiration date	Classification
First Warrant	9,216	$	65.92	Q4 2019	Equity
Second Warrant	41,177	$	6.80	Q2 2023	Equity
Hercules Warrant						41,177	$	6.80	Q2 2023	Equity
2018 Public Offering Warrants	3,616,944	$	9.60	Q1 2023	Liability	3,616,944	$	9.60	Q1 2023	Liability
Private Placement Warrants	932,812	$	4.52	Q1 2024	Equity	932,812	$	4.52	Q1 2024	Equity
Pre-Funded Warrants	531,250	$	0.08	Q1 2039	Equity	531,250	$	0.08	Q1 2039	Equity
	5,131,399					5,122,183

~~First and Second~~Hercules Warrant

The exercise price and the number of shares are subject to adjustment upon a merger event, reclassification of the shares of common stock, subdivision or combination of the shares of common stock or certain dividends payments. The Company determined that the ~~First and Second~~Hercules Warrant should be equity classified in accordance with ASC 480,Distinguishing Liabilities from Equity ("ASC 480") for all periods presented.

2018 Public Offering Warrants

In January 2018, the Company entered into two underwriting agreements, the first relating to the public offering of 6,670,625 shares of the Company’s common stock, par value $0.001 per share, and accompanying warrants to purchase up to 3,335,313 shares of common stock (“2018 Public Offering Warrants”). The exercise price and the number of shares are subject to adjustment upon a merger event, reclassification of the shares of common stock, subdivision or combination of the shares of common stock or certain dividends payments. In the event of an “Acquisition,” defined generally to include a merger or consolidation resulting in the sale of 50% or more of the voting securities of the Company, the sale of all, or substantially all, of the assets or voting securities of the Company, or other change of control transaction, as defined in the 2018 Public Offering Warrants, the Company will be obligated to use its best efforts to ensure that the holders of the 2018 Public Offering Warrants receive new warrants from the surviving or acquiring entity (the “Acquirer”). The new warrants to purchase shares in the Acquirer shall have the same expiration date as the 2018 Public Offering Warrants and a strike price that is based on the proportion of the value of the Acquirer’s stock to the Company’s common stock. If the Company is unable, despite its best efforts, to cause the Acquirer to issue new warrants in the Acquisition as described above, then, if the Company’s stockholders are to receive cash in the Acquisition, the Company will settle the 2018 Public Offering Warrants in cash and if the Company’s stockholders are to receive stock in the Acquisition, the Company will issue shares of its common stock to each Warrant holder.

The Company determined that the 2018 Public Offering Warrants should be liability classified in accordance with ASC 480. As the 2018 Public Offering Warrants are liability-classified, the Company remeasures the fair value ~~of the Warrants~~ at each reporting date. The Company initially recorded the 2018 Public Offering Warrants at their estimated fair value of approximately $18.2 million. In connection with the Company's remeasurement of the 2018 Public Offering Warrants to fair value, the Company recorded income of approximately ~~$3.9~~$0.8 million and ~~$5.5~~expense of approximately $5.8 million for the three months ended ~~June 30,~~March 31, 2020 and 2019, ~~and 2018, respectively, and expense of $1.9 million and $2.3 million of income for the six months ended June 30, 2019 and June 30, 2018,~~ respectively. The fair value of the warrant liability is approximately $1.7 million and $2.5 million as of March 31, 2020 and December 31, 2019, respectively.

~~warrant liability is approximately $5.4 million and $3.5 million as of June 30, 2019 and December 31, 2018, respectively. See~~ ~~Note 3. Fair Value Measurements.~~

The following table details the assumptions used in the Monte Carlo simulation models used to estimate the fair value of the Warrant Liability as of ~~June 30, 2019~~March 31, 2020 and December 31, ~~2018,~~2019, respectively:


	June 30, 2019			December 31, 2018			March 31, 2020			December 31, 2019
Stock price	$	3.92		$	2.32		$	1.72		$	2.07
Volatility	121.5		%	111.3		%	50.0% - 124.5%			50.0% - 116.6%
Remaining term (years)	3.6			4.1			2.8			3.1
Expected dividend yield	—			—			—			—
Risk-free rate	1.7		%	2.4%-2.5%			0.3		%	1.6		%
Range of annual acquisition event probability	15.0%-30.0%			0.0%-30.0%
Annual acquisition event probability							30.0		%	20.0		%

Private Placement and Prefunded Warrants

The exercise price of the warrants is subject to appropriate adjustment in the event of stock dividends, subdivisions, stock splits, stock combinations, reclassifications, reorganizations or a change of control affecting our common stock. The Company determined that the Private Placement Warrants and the Pre-Funded Warrants should be equity classified in accordance with ASC 480 for the period ended ~~June 30, 2019.~~March 31, 2020. The Company also determined that the Pre-Funded Warrants should be included in the determination of basic earnings per share in accordance with ASC 260, Earnings per Share.

8.9. Stock and employee benefit plans

The Company issues stock options and restricted stock units (“RSUs”) to employees, which generally vest ratably over a four year service period. The Company measures the fair value of stock options on the date of grant using the Black-Scholes option pricing model. The Company measures the fair value of RSUs on the date of grant using the underlying common stock fair value.

Stock-based compensation expense

Total stock-based compensation expense is recognized for stock options and ~~restricted stock awards granted to employees and non-employees and has been reported in the Company’s condensed consolidated statements of operations~~RSUs is as follows (in thousands):


	Three Months Ended June 30,				Six Months Ended June 30,				Three Months Ended March 31,
	2019		2018		2019		2018		2020		2019
Research and development	$	170	$	159	$	352	$	300	160		182
General and administrative	304		433		551		936		$	224	$	247
Total	$	474	$	592	$	903	$	1,236	$	384	$	429

Stock options

The following table summarizes stock option activity ~~for employees and non-employees~~ (shares in thousands):

Shares Weighted-
Average
Exercise
Price Weighted-
Average
Remaining
Contractual
Term (years) Aggregate
Intrinsic
Value
Outstanding at December 31, 2018 893
$ 18.79

$ —
Granted 501
$ 4.66

Exercised (5 ) $ 4.32

Cancelled (104 ) $ 25.24

Outstanding at June 30, 2019 1,285
$ 12.81
8.32 $ 1,435
Exercisable at June 30, 2019 402
$ 25.57
6.38 $ —

~~Performance-based awards~~



	Shares		Weighted-Average Exercise Price		Weighted-Average Remaining Contractual Term (years)	Aggregate Intrinsic Value
Outstanding at December 31, 2019	1,323		$	11.65		$	—
Granted	66		$	1.99
Exercised	—		$	—
Cancelled	(19	)	$	4.85
Outstanding at March 31, 2020	1,370		$	11.28	7.90	$	—
Exercisable at March 31, 2020	585		$	18.90	6.72	$	—

RSUs

The Company granted stock awards to certain employees, executive officers and consultants, which contain performance-based vesting criteria. Milestone events are specific to the Company’s corporate goals, which include, but are not limited to, certain clinical development milestones, business development agreements, and capital fundraising events. Stock-based compensation expense associated with these performance-based stock options is recognized if the performance conditions are considered probable of being achieved, using management’s best estimates. The Company determined that none of the performance-based milestones were probable of achievement during the three and six months ended June 30, 2019, and did not recognize stock-based compensation expense for this period. As of June 30, 2019, there were 7,042 performance-based common stock awards outstanding for which the probability of achievement was not deemed probable.following table summarizes RSU activity (shares in thousands):



	Shares	Weighted-Average Grant Date Fair Value
Outstanding as of December 31, 2019	—	$	—
Granted	45	$	1.98
Vested	—	$	—
Forfeited/cancelled	—	$	—
Outstanding as of March 31, 2020	45	$	1.98

Employee stock purchase plan

OnIn February ~~10,~~ 2014, the Company’s board of directors adopted the 2014 Employee Stock Purchase Plan and subsequently amended the plan in June 2018 (the ~~“2014 ESPP”~~“ESPP”). The ~~2014~~ ESPP ~~as amended,~~ authorizes the issuance of up to 337,597 shares of common stock to participating eligible ~~employees. The 2014 ESPP~~employees and provides for two six-month ~~option periods commencing on January 1 and ending June 30, and commencing July 1 and ending December~~offering periods. As of March 31, ~~of each calendar year. The stock-based compensation expense related to the 2014 ESPP was insignificant~~2020, there were 217,985 shares remaining for ~~the three and six months ended June 30, 2019 and 2018, respectively.~~

~~9. Commitments and contingencies~~

~~Lease commitments~~

In May 2019, the Company entered into a lease extension for office and laboratory space through February 2025. The Company also has a lease for additional office space through February 2020. The right to use asset and lease liability were calculated using an incremental borrowing rate of 8.25% and 10%, respectively. For the three months ended June 30, 2019 and 2018 rent expense was $0.3 million and $0.4 million, respectively. For the six months ended June 30, 2019 and 2018 rent expense was $0.7 million and $0.8 million, respectively.

~~In March 2019, the Company entered into a sublease agreement for a portion of the office space lease through February 2020. Since the Company retained its obligations~~future issuance under the ~~sublease, it did not adjust the lease liability, however the sublease is being reflected as a reduction of lease expense.~~

~~Maturities of lease liabilities are as follows (in thousands):~~

June 30, 2019
2019 $ 821
2020 1,477
2021 1,474
2022 1,510
2023 and thereafter 3,401
Total lease payments 8,683
Less imputed interest (1,777 )
Total $ 6,906

At June 30, 2019 and December 31, 2018, the Company has an outstanding letter of credit of $0.3 million with a financial institution related to a security deposit for the office and lab space lease, which is secured by cash on deposit and expires on February 28, 2025.

~~Litigation~~

~~Pending Litigation:~~

on March 29, 2018. Defendants filed a motion to dismiss on May 14, 2018. The lead plaintiff filed an opposition to defendants’ motion to dismiss on June 28, 2018, as well as a motion to strike certain documents attached to defendants’ motion to dismiss, on June 29, 2018. Defendants filed a reply in further support of the dismissal motion, and an opposition to plaintiffs’ motion to strike, on July 30, 2018. The court held oral argument on the motion to dismiss and motion to strike on September 25, 2018. On December 6, 2018, the court granted defendants’ motion to dismiss and, because the court’s decision did not consider the documents plaintiffs sought to strike, did not rule on plaintiffs’ motion to strike. On January 7, 2019, plaintiffs filed a notice of appeal in the District of Massachusetts to appeal the court’s order granting defendants’ motion to dismiss. The appeal, captioned ~~Yuksel v. Genocea Biosciences, Inc., et al.~~, U.S. Court of Appeal for the First Circuit, Case No. 19-1036, was docketed in the First Circuit on January 15, 2019. By order dated January 29, 2019, the First Circuit set a deadline of March 11, 2019 for plaintiffs’ opening brief. Shortly thereafter, however, plaintiffs made a settlement offer to defendants, and the parties subsequently entered into a settlement agreement and general release on April 22, 2019. In connection with the settlement agreement, the parties fully and finally resolved the ~~Emerson~~ Action, including the entry of a general release, and plaintiffs agreed to request a voluntary dismissal of the appeal with prejudice pursuant to Federal Rule of Appellate Procedure 42(b). On May 9, 2019, plaintiffs filed the voluntarily dismissal motion. The Court dismissed the ~~Emerson~~ ~~Action on May 23, 2019.~~

~~Kahr v. William Clark et al.~~, U.S. District Court (Del.), Civil Action No. 18-cv-00186-MN. On January 31, 2018, Barry Kahr, a purported Genocea shareholder, filed a putative shareholder derivative complaint against certain of the Company’s officers and directors (including certain former officers and directors), naming the Company as the nominal defendant. The complaint alleged violations of the Securities Exchange Act of 1934, as amended, and Rule 14a-9 in connection with disclosures made in the Company’s Schedule 14A Proxy Statement, filed with the SEC on April 21, 2017. The complaint also alleged claims for breach of fiduciary duty, unjust enrichment, and waste of corporate assets. On May 1, 2018, the parties filed a joint stipulation and proposed order agreeing to stay the action until, ~~inter alia, the entry of an order granting or denying any motion to dismiss the~~ ~~Emerson~~ ~~Action. On May 9, 2018, the court entered the joint stipulation agreeing to stay the action.~~

~~On August 10, 2018, the parties, along with the plaintiff from the~~ ~~Howard~~ ~~action, detailed below, filed a joint stipulation and proposed order agreeing to,~~ ~~inter alia, consolidate the~~ ~~Kahr~~ ~~and~~ ~~Howard~~ ~~actions into an action captioned~~ ~~In re Genocea Biosciences, Inc. Derivative Litigation~~, U.S. District Court (Del.), Civil Action No. 18-cv-00186-MN (the “Genocea Consolidated Derivative Action”). The joint stipulation also proposed to stay the consolidated action pursuant to the same terms as the stay order entered in ~~Kahr~~, and allow the Rosen Law Firm, P.A. and Gainey McKenna & Egleston to serve as co-lead counsel for plaintiffs in the consolidated action. On August 24, 2018, the court entered the joint stipulation agreeing to consolidate the ~~Kahr~~ ~~and~~ ~~Howard~~ ~~actions, and stay the Genocea Consolidated Derivative Action. On February 4, 2019, the parties filed a joint stipulation and proposed order agreeing to extend the stay order until,~~ ~~inter alia, the resolution of the First Circuit appeal in the~~ ~~Emerson~~ ~~Action. On February 5, 2019, the court entered the joint stipulation agreeing to extend the stay. However, following the dismissal of the~~ ~~Emerson~~ ~~action, the plaintiff from the~~ ~~Kahr~~ ~~action, along with the plaintiff from the~~ ~~Howard~~ ~~action, detailed below, voluntarily dismissed the Genocea Consolidated Derivative Action on July 1, 2019. The court closed the~~ ~~Kahr~~ ~~action on July 1, 2019.~~

~~Howard v. William Clark et al.~~, U.S. District Court (Del.), Civil Action No. 18-cv-00912-MN. On June 20, 2018, Julie Howard, a purported Genocea shareholder, filed a putative shareholder derivative complaint against certain of the Company’s officers and directors (including one former officer), naming the Company as the nominal defendant. The complaint alleged violations of the Securities Exchange Act of 1934, as amended, and Rule 14a-9 in connection with disclosures made in the Company’s Schedule 14A Proxy Statement, filed with the SEC on April 21, 2017. The complaint also alleged claims for breach of fiduciary duty, unjust enrichment, and waste of corporate assets. As detailed above, the ~~Howard~~ ~~action was consolidated with the~~ ~~Kahr~~ ~~action into the Genocea Consolidated Derivative Action, which the court stayed until,~~ ~~inter alia, the resolution of the First Circuit appeal in the~~ ~~Emerson~~ ~~Action. Following the dismissal of the~~ ~~Emerson~~ ~~action, however, the plaintiff from the~~ ~~Kahr~~ ~~action voluntarily dismissed the Genocea Consolidated Derivative Action on July 1, 2019. The court closed the~~ ~~Howard~~ ~~action on July 1, 2019.~~plan.

10. Net loss per share

~~The Company computes basic~~Basic and diluted net loss per share ~~using a methodology that gives effect to the impact of outstanding participating securities (the “two-class method”). For both~~was calculated as follows for the three months ended March 31, 2020 and six-month periods ended June 30, 2019 and 2018, respectively, there is no income allocation required under the two-class method or dilution attributed to weighted average shares outstanding in the calculation of diluted loss per share.2019:



	Three months ended March 31,
	2020			2019
Basic net loss per share:
Numerator:
Net loss (in thousands)	$	(12,853	)	$	(15,567	)
Denominator:
Weighted average common stock outstanding - basic (in thousands)	28,141			12,713
Dilutive effect of shares of common stock equivalents resulting from common stock options and restricted stock units	—			—
Weighted average common stock outstanding - diluted	28,141			12,713
Net loss per share - basic and diluted	$	(0.46	)	$	(1.22	)

The following common stock equivalents outstanding as of March 31, 2020 and 2019, presented on an as converted basis, were excluded from the calculation of net loss per share for the periods presented, due to their anti-dilutive effect (in thousands):



	Three Months Ended March 31,
	2020	2019
Warrants	4,591	4,600
Stock options	1,370	1,299
RSUs	45	—
Total	6,006	5,899

Six Months Ended June 30,
2019 2018
Stock options 1,285
713
Warrants 4,600
3,668
ESPP 265
—
Total 6,150
4,381

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

The following information should be read in conjunction with the unaudited consolidated financial information and the notes thereto included in this Quarterly Report on Form 10-Q. The following disclosure contains forward-looking statements that involve risk and uncertainties. Our actual results and timing of certain events could differ materially from those anticipated in these forward-looking statements as a result of certain factors, including those discussed in our Annual Report on Form 10-K.

Overview

We are a biopharmaceutical company that seeks to discover and develop novel cancer immunotherapies using ~~the ATLAS™~~our ATLAS^TM proprietary discovery platform. The ATLAS platform profiles each patient's CD4⁺and CD8⁺ T cell immune responses to every potential target or “antigen” in that patient's tumor. We believe that this approach optimizes antigen selection for immunotherapies such as cancer vaccines and cellular therapies ~~because it identifies~~by identifying the antigens to which ~~a patient’s T cells already mount anti-tumor responses. We~~the patient can respond. Consequently, we believe that ATLAS could lead to more immunogenic and efficacious cancer immunotherapies.

Our most advanced program is GEN-009, a personalized neoantigen cancer vaccine, for which we are conducting a Phase 1/2a clinical trial. The GEN-009 program uses ATLAS to identify neoantigens, or immunogenic tumor mutations unique to each patient, for inclusion in each patient's GEN-009 vaccine. We are also advancing GEN-011, a neoantigen-specific adoptive T cell therapy program ~~as well as GEN-010, a follow-on neoantigen vaccine program.~~that also relies on ATLAS. We expect to file an IND for GEN-011 in the second quarter of 2020.

ATLAS Platform

Harnessing and directing the T cell arm of the immune system to kill tumor cells is increasingly viewed as having potential in the treatment of many cancers. This approach has ~~shown efficacy in~~been effective against hematologic malignancies and, more recently, certain solid tumors. Vaccines or cellular therapies employing this approach must target specific differences from normal tissue present in a tumor, such as antigens arising from genetic mutations. However, the discovery of optimal antigens for such immunotherapies has been particularly challenging for two reasons. First, the genetic diversity of human T cell responses means that effective antigens vary from person to person. Second, the number of candidate antigens can be very large, with up to thousands of candidates per patient in some cancers. An effective antigen selection system must therefore account both for each patient's tumor and for their T cell repertoire.

~~The~~ ATLAS ~~platform is designed to do just this. We believe that ATLAS represents the most comprehensive, accurate, and high-throughput system for~~achieves effective antigen ~~discovery in the biopharmaceutical industry. ATLAS employs~~selection by employing components of the T cell arm of the human immune system from each ~~patient that it profiles in a laboratory setting.~~patient. Using ATLAS, we can measure ~~that~~each patient's T cell responses to a comprehensive set of candidate neoantigens, tumor-associated antigens orand tumor-associated viral antigens for ~~any individual’s~~their own cancer, allowing us to select those targets associated with the anti-tumor T cell responses that may kill that individual's cancer.

~~The~~ We believe that ATLAS represents the most comprehensive and accurate system for antigen discovery. Further, we believe ATLAS identifies a novel candidate antigen profile, that of inhibitory T cell ~~responses we have seen appear~~responses. Previously, all candidate antigens were thought either to ~~challenge previous assumptions in the field - specifically, that all neoantigens are either “good ,” meaning~~be targets of effective anti-tumor responses (stimulatory), or irrelevant. ~~Using~~However, using ATLAS, we have ~~profiled approximately 200 cancer patients' CD4~~identified inhibitory antigens we call Inhibigens^+TM, which are shown to promote tumor progression in preclinical studies. We have also discovered that an antigen can be stimulatory in one patient and ~~CD8~~⁺ ~~T cell responses to their tumors. At the meeting of the Society for Immunotherapy of Cancer~~inhibitory in ~~November 2018, we presented data from preclinical research in which ATLAS-identified inhibitory neoantigens promoted tumor progression,~~another, reinforcing the importance of ~~accounting for~~selecting each patient's ~~pre-existing immune responses in antigen selection, and suggesting the high stakes for choosing the right~~potentially immunogenic antigens. ~~We are not aware of another platform that is capable of employing this comprehensive neoantigen profiling.~~

The ATLAS portfolio comprises three patent families. The first two families comprise issued U.S. patents, with patent terms until at least 2031 and 2030, respectively, as well as ~~issued~~granted foreign patents and pending U.S. and foreign applications. The third family is directed to ATLAS-based methods for cancer diagnosis, prognosis and patient selection, as well as related compositions. This patent family currently comprises a pending ~~PCT application~~applications in eleven foreign jurisdictions and a pending U.S. application. Patents issuing from these applications are expected to have a patent term until at least March 2038.

Our Immuno-Oncology Programs

Our cancer immunotherapies ~~consist of vaccines~~include a vaccine that ~~are~~is designed to educate T cells to recognize and attack specific cancer targets, ~~as well as~~and a cellular ~~therapies~~therapy intended to introduce T cells that have been educated to attack these targets, thereby killing cancer cells. We are developing personalized cancer vaccines using our proprietary ATLAS platform to identify patient-specific neoantigens that are associated with that individual's pre-existing immune responses to a tumor.

Data published in recent years indicate that an individual’s response to neoantigens drives the efficacy of immune checkpoint inhibitor, or ICI, therapy and that it is possible to vaccinate an individual against his or her own neoantigens.targets. We believe that neoantigen vaccines could be used in combination with existing treatment approaches for cancer ~~including ICI therapy,~~ to potentially direct and enhance an individual’s T cell response to his or her cancer, thereby potentially effecting better clinical outcomes. ~~Data~~We also ~~support the potential of~~believe that isolating and expanding T cell populations targeting specific neoantigens ~~for therapeutic~~through adoptive cell therapy could provide meaningful clinical benefit.

The following describes our active immuno-oncology programs in development:

Our lead ~~immuno-oncology~~ program, GEN-009, is an adjuvanted neoantigen peptide vaccine candidate. Using ATLAS to identify specific neoantigens, we ~~then~~ manufacture a personalized vaccine for each patient using only those neoantigens determined by ATLAS to be stimulatory to that patient's anti-tumor immune ~~system.~~

~~The following table describes our active immuno-oncology programs in development:~~



~~Vaccine~~ ~~Candidate~~	~~Program~~	~~Stage of~~ ~~Development~~	~~Next Milestones~~	~~Anticipated Timeline~~
~~GEN-009~~	~~Neoantigen cancer vaccine~~	~~Phase 1/2a~~	~~Additional monotherapy results from Part A of clinical trial~~ ~~Preliminary results from Part B of clinical trial~~	~~Fourth quarter of 2019~~ ~~Mid-2020~~
~~GEN-011~~	~~Neoantigen adoptive T cell therapy~~	~~Preclinical~~	~~IND filing~~ ~~Preliminary results of clinical trial~~	~~First half of 2020~~ ~~Second half of 2020~~
~~GEN-010~~	~~Neoantigen cancer vaccine~~	~~Preclinical~~	~~Next-generation delivery technology~~	~~Ongoing~~

responses. We are currently conducting a Phase 1/2a clinical trial for GEN-009 across a range of solid tumor types:

Part A of the trial is assessing the safety and immunogenicity of GEN-009 as monotherapy in certain cancer patients with no evidence of disease; and

Part B of the trial, for which we have ~~recently initiated,~~commenced dosing patients, is designed to assess the safety, immunogenicity, and preliminary antitumor activity of GEN-009 in combination with ICI therapy in patients with advanced or metastatic tumors.

~~At the Annual Meeting of the American Society of Clinical Oncology~~The patients in ~~June 2019, we presented the first peer-reviewed data from~~ Part A of the ~~ongoing clinical trial.~~trial had little to no detectable tumor at the time of vaccination with GEN-009, but were still at risk of relapse. In the data from the ~~first five evaluable patients:~~eight dosed patients we observed the following:


•	100% of patients had measurable CD4⁺and CD8⁺ T cell responses to their GEN-009 vaccine;

Responses were detected ~~for 91%~~against 99% of the administered vaccine neoantigens (N=~~5);~~88 administered antigens), a response rate in excess of that which has been reported previously in response to candidate neoantigen vaccines;


•	GEN-009 elicited CD8⁺ T cell responses ex vivo, which is a measure of T cell effector function, for ~~47%~~41% of vaccine neoantigens ~~(N=5);~~and CD4⁺ T cell responses to 51% of neoantigens;


•	GEN-009 elicited broad immune responses using an in vitro stimulation assay, which is a measure of central memory responses, with ~~86%~~87% of neoantigens eliciting a CD4⁺ response ~~(N=5)~~ and ~~33%~~57% of neoantigens eliciting a CD8⁺ ~~response (N=2); and~~response;

GEN-009 was well tolerated, with no dose-limiting toxicities ~~observed.~~observed; and

Through April 8, 2020, only one of the eight vaccinated patients has developed a recurrent tumor.

We believe the above data confirms the potential antigen selection advantages of ATLAS.

~~We currently anticipate reporting~~In the ~~first GEN-009 results from~~fourth quarter of 2019, we began dosing patients for Part B of our GEN-009 study. We anticipate reporting these preliminary clinical results in the ~~trial in mid-2020. As with any open label study, we may slow or pause accrual for Part B~~third quarter of 2020. We believe that the current patients enrolled are sufficient to ~~evaluate a smaller set of patients in an effort to assure that~~determine whether a preliminary clinical signal can be seen, therefore, we have paused enrollment in our GEN-009 Part B trial. Upon review of the preliminary clinical results, we will consider whether it is ~~seen.~~appropriate to continue the study.

~~In addition to GEN-009, we~~We also are advancing ~~preclinical work on~~ GEN-011, an adoptive T cell therapy tospecific for neoantigens identified by ~~ATLAS, for which we~~ATLAS. Adoptive T cell therapies offer an alternative treatment in solid tumors. GEN-011 extracts and specifically expands ATLAS-identified neoantigen-specific T cells from each patient's peripheral blood. We expect to file an IND application for GEN-011 with the U.S. Food and Drug Administration (“FDA”) in the ~~first half~~second quarter of 2020, with preliminary clinical results anticipated in the ~~second~~first half of ~~2020.~~2021.

We continue to conduct research, principally to explore Inhibigen^TM biology and ways to further strengthen ATLAS. We also continue to explore ~~GEN-010,~~additional program opportunities. The COVID-19 pandemic has materially affected our ~~vaccine candidate employing next-generation antigen delivery technology,~~ability to continue such efforts, however, so we cannot provide specific timelines for these efforts to translate into new clinical candidates, which ~~we may advance to provide an opportunity for better immunogenicity and/or efficiency of production.~~might include

~~In addition, we are using ATLAS to pursue discovery of novel candidate antigens for~~

non-personalized cancer ~~immunotherapies. Such programs could target~~immunotherapies targeting shared neoantigens, non-mutated ~~shared~~ tumor-associated antigens, ~~and~~ cancers of viral origin such as cancers driven by Epstein-Barr ~~Virus infection.~~virus infection and Inhibigens^TM.

Financing and business operations

We commenced business operations in August 2006. We have financed our operations primarily through the issuance of our equity securities, debt financings, and amounts received through grants. As of ~~June 30, 2019,~~March 31, 2020, we had received an aggregate of ~~$396.8~~$399.7 million in gross proceeds from the issuance of equity securities and gross proceeds from debt facilities and an aggregate of $7.9 million from grants. At ~~June 30, 2019,~~March 31, 2020, our cash and cash equivalents were ~~$58.7~~$26.5 million.

Since inception, we have incurred significant operating losses. ~~Our net losses were $22.1 million for the six months ended June 30, 2019, and our accumulated deficit was $314.1 million as of June 30, 2019.~~ We expect to incur significant expenses and increasing operating losses for the foreseeable future. Our net losses may fluctuate significantly from quarter-to-quarter and year-to-year. We will need to generate significant revenue to achieve profitability, and we may never do so.

In October 2019, we entered into a purchase agreement with Lincoln Park Capital (“LPC”) pursuant to which LPC purchased $2.5 million of shares of our common stock at a purchase price of $2.587 per share. In addition, for a period of 30 months, we have the right, at our sole discretion, to sell up to an additional $27.5 million of our common stock based on prevailing market prices of our common stock at the time of each sale. In consideration for entering into the purchase agreement, we issued 289,966 shares of our common stock to LPC as a commitment fee. The purchase agreement limits our sales of shares of common stock to LPC to 5,227,323 shares of common stock, representing 19.99% of the shares of common stock outstanding on the date of the purchase agreement. The purchase agreement also prohibits us from directing LPC to purchase any shares of common stock if those shares, when aggregated with all other shares of our common stock then beneficially owned by LPC and its affiliates, would result in LPC and its affiliates having beneficial ownership, at any single point in time, of more than 9.99% of the then total outstanding shares of our common stock. In January 2020, we sold 186,986 shares of common stock to LPC, for net proceeds of approximately $0.4 million.

In June 2019, we completed an underwritten public offering in which we sold ~~10.5 million~~10,500,000 shares of our common stock at a price of $3.50 per share, for gross proceeds of approximately $36.8 million. This underwritten public offering also included an overallotment option for the underwriters for ~~1.6 million~~1,575,000 shares, which they exercised in full on June 26, 2019. This generated additional gross proceeds of $5.5 million. ~~The Company~~We incurred approximately $3.9 million of offering-related expenses, resulting in total net proceeds of $38.4 million.

In February 2019, we completed a private placement financing transaction in which we issued ~~Shares, Pre-funded Warrant Shares~~shares of our common stock, pre-funded warrants to purchase shares of our common stock, and ~~Warrants~~warrants to purchase shares of our common stock for gross cash proceeds of $15.0 million. We incurred $1.2 million of offering-related expenses, resulting in total net ~~cash~~ proceeds of approximately $13.8 million.

As reflected in our consolidated financial statements, we used cash to fund operating activities of $13.8 million for the three months ended March 31, 2020 and had $26.5 million available in cash and cash equivalents at March 31, 2020. In addition, our net losses were $12.9 million for the three months ended March 31, 2020, and we had an accumulated deficit of $343.8 million. We anticipate that we will continue to incur significant operating losses for the foreseeable future as we continue to develop our product candidates. Until such time, if ever, as we attempt to generate substantial product revenue and achieve profitability, we expect to finance our cash needs through a combination of equity offerings and strategic transactions, and other sources of funding. If we are unable to raise additional funds when needed, we may be required to implement further cost reduction strategies, including ceasing development of GEN-009, GEN-011, and other corporate programs and activities. These factors, combined with our forecast of cash required to fund operations for a period of at least one year from the date of issuance of these consolidated financial statements, raise substantial doubt about our ability to continue as a going concern.

We believe that our cash and cash equivalents at March 31, 2020 are sufficient to support our operating expenses and capital expenditure requirements into the first quarter of 2021.

Costs related to clinical trials can be unpredictable and there can be no guarantee that our current balances of cash and cash equivalents combined with proceeds received from other sources, will be sufficient to fund our trials or operations through this period. These funds will not be sufficient to enable us to conduct pivotal clinical trials for, seek marketing approval for, or commercially launch GEN-009, GEN-011 or any other product candidate. Accordingly, we will be required to obtain further funding through public or private equity offerings, ~~debt financings,~~ collaboration and licensing arrangements, or other sources. Adequate additional financing may not be available to us on acceptable terms, or at all, which could result in a decision to pause or delay development or advancement of clinical trials for one or more of our product candidates. Similarly, we may decide to pause or delay development or advancement of clinical trials for one or more of our product candidates if we believe that such development or advancement is imprudent or impractical.

Financial Overview

Research and development expenses

Research and development expenses consist primarily of costs incurred to advance our preclinical and clinical candidates, which include:

~~personnel-related expenses, including salaries, benefits, stock-based compensation expense,~~salary and ~~travel;~~related expenses;

expenses incurred under agreements with contract research organizations (“CROs”), contract manufacturing organizations (“CMOs”), consultants, and other vendors that conduct our clinical trials and preclinical activities;

costs of acquiring, developing, and manufacturing clinical trial materials and lab supplies; and

facility costs, depreciation, and other expenses, which include direct and allocated expenses for rent and maintenance of facilities, insurance, and other supplies.

We expense internal research and development costs to operations as incurred. Nonrefundable advanced payments for goods and services that will be used in future research and development activities are expensed when the activity has been performed or when the goods have been received rather than when the payment is made.

The following table identifies research and development expenses for our product candidates as follows (in thousands):



	Three Months Ended March 31,
	2020		2019
Phase 1/2a programs	$	4,793	$	4,720
Discovery and pre-IND	3,809		788
Other research and development	1,385		952
Total research and development	$	9,987	$	6,460

Three Months Ended June 30, Six Months Ended June 30,
2019 2018 2019 2018
Discovery and pre-IND $ 1,253
$ 4,452
$ 2,041
$ 10,511
Phase 1/2a programs 4,588
—
9,308
—
Other research and development 1,008
864
1,960
2,080
Total research and development $ 6,849
$ 5,316
$ 13,309
$ 12,591

Phase 1/2a programs are Phase 1 or Phase 2 development activities. Discovery and ~~Pre-IND~~pre-IND includes costs incurred to support our discovery research and translational science efforts up to the initiation of Phase 1 development. ~~Phase 1/2a programs are Phase 1 or Phase 2 development activities.~~ Other research and development ~~includes~~include costs that are not specifically allocated to active product candidates, including facilities costs, depreciation expense, and other costs.

We expect that our overall research and development expenses will increase due to our continued development of our clinical operations and our supply chain capabilities for our GEN-009 program, as well as our advancement of GEN-011 through preparation and submission of an IND and subsequent initiation of a clinical trial.

General and administrative expenses

General and administrative expenses consist ~~principally~~primarily of salaries and related ~~costs~~expenses for personnel ~~including stock-based compensation and travel,~~ in executive and other administrative functions. Other general and administrative expenses include facility costs, ~~communication expenses,~~ and professional fees associated with consulting, corporate and intellectual property legal expenses, ~~consulting,~~ and accounting services.

We anticipate that our general and administrative expenses will increase in the future to support the continued research and development of our product candidates and to operate as a public company. Additionally, if and when we believe regulatory approval of our first product candidate appears likely, we anticipate that we will increase costs in preparation for commercial operations.

Other income (expense)

Other income (expense) consists of the change in ~~warranty~~warrant liability, interest expense, net of interest income, and other expense for miscellaneous items, such as the transaction expenses.

Critical Accounting Policies and Significant Judgments and Estimates

We believe that several accounting policies are important to understanding our historical and future performance. We refer to these policies as critical because these specific areas generally require us to make judgments and estimates about matters that are uncertain at the time we make the estimate, and different estimates—which also would have been reasonable—could have been used. The preparation of financial statements in conformity with U.S. GAAP requires us to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. On an ongoing basis, we evaluate estimates, which include prepaid and accrued research and development expenses ~~stock-based compensation expense,~~ and the fair value of our warrant liability. We base our estimates on historical experience and other market-specific or other relevant assumptions that we believe to be reasonable under the circumstances. Actual results may differ materially from those estimates or assumptions.

There were no changes to our critical accounting policies during the ~~six~~three months ended ~~June 30, 2019,~~March 31, 2020, as compared to ~~the~~ those identified in the Company's Annual Report on Form 10-K for the fiscal year ended December 31, ~~2018.~~2019. It is important that the

discussion of our operating results that follow be read in conjunction with the critical accounting policies disclosed in our Annual Report on Form 10-K, as filed with the SEC on February ~~28, 2019.~~13, 2020.

Results of Operations

Comparison of the three months ended ~~June 30,~~March 31, 2020 and 2019 ~~and June 30, 2018~~


	Three Months Ended June 30,						Increase			Three Months Ended March 31,						Increase
(in thousands)	2019			2018			(Decrease)			2020			2019			(Decrease)
Operating expenses:
Research and development	$	6,849		$	5,316		$	1,533		$	9,987		$	6,460		$	3,527
General and administrative	3,217			4,472			(1,255		)	3,388			3,017			371
Total operating expenses	10,066			9,788			278			13,375			9,477			3,898
Loss from operations	(10,066		)	(9,788		)	278			(13,375		)	(9,477		)	3,898
Other income (expense):
Change in fair value of warrants	3,870			5,498			1,628			781			(5,787		)	6,568
Interest expense, net	(299		)	(241		)	58			(259		)	(302		)	43
Other income (expense)	—			93			93			—			(1		)	1
Total other income	3,571			5,350			1,779			522			(6,090		)	6,612
Net loss	$	(6,495	)	$	(4,438	)	$	2,057		$	(12,853	)	$	(15,567	)	$	(2,714	)

Research and development expenses

Research and development expenses increased ~~$1.5~~$3.5 million in the three months ended ~~June 30, 2019,~~March 31, 2020, as compared to the three months ended ~~June 30, 2018.~~March 31, 2019. The increase was ~~primarily~~largely due to increased external manufacturing costs ~~to support GEN-009~~of approximately $2.3 million, increased headcount-related costs of approximately $0.5 million, increased clinical ~~trials partially offset by decreased consulting expenses.~~trial costs of approximately $0.3 million, and increased lab supplies costs of approximately $0.2 million.

General and administrative expenses

General and administrative expenses ~~decreased $1.3~~increased $0.4 million in the three months ended ~~June 30, 2019,~~March 31, 2020, as compared to the three months ended ~~June 30, 2018.~~March 31, 2019. The ~~decrease~~increase was primarily due to ~~a reduction in~~increased legal ~~expenses partially offset by~~costs of approximately $0.2 million, increased ~~headcount.~~consulting and professional services costs of approximately $0.1 million, and increased rent expense of approximately $0.1 million.

Change in fair value of warrants

Change in fair value of warrants reflects the non-cash change in the fair value of ~~warrants. Certain warrants issued in~~the 2018 Public Offering Warrants, which were recorded at their fair value on the date of issuance and are remeasured at the end of each reporting period. The increase in the change in the fair value of warrants was primarily the result of a decrease in our stock price in the three months ended March 31, 2020 as compared to an increase in our stock price in the three months ended March 31, 2019.

Interest expense, net

Interest expense, net, consists primarily of interest expense on our long-term debt facilities, ~~and non-cash interest related to the amortization of debt discount and issuance costs, offset by interest earned on our cash equivalents.~~

~~Comparison of the six months ended June 30, 2019 and June 30, 2018~~

Six Months Ended June 30, Increase
(in thousands) 2019 2018 (Decrease)
Operating expenses:
   Research and development $ 13,309
$ 12,591
$ 718
   General and administrative 6,234
7,581
(1,347 )
   Total operating expenses 19,543
20,172
(629 )
Loss from operations (19,543 ) (20,172 ) (629 )
Other income (expense):
   Change in fair value of warrants (1,917 ) 199
(2,116 )
   Interest expense, net (601 ) (442 ) 159
   Other income (expense) (1 ) 87
(88 )
Total other expense (2,519 ) (156 ) 2,363
Net loss $ (22,062 ) $ (20,328 ) $ 1,734

~~Research and development expenses~~

Research and development expenses increased $0.7 million in the six months ended June 30, 2019, as compared to the six months ended June 30, 2018. The increase was primarily due to higher external manufacturing costs to support GEN-009 clinical trials and increased headcount-related costs to support GEN-009 clinical trials, partially offset by decreased consulting expenses.

~~General and administrative expenses~~

General and administrative expenses decreased $1.3 million in the six months ended June 30, 2019, as compared to the six months ended June 30, 2018. The decrease was primarily due to a reduction in legal expenses partially offset by increased headcount.

~~Change in fair value of warrants~~

Change in fair value of warrants reflects non-cash change in fair value of warrants. Certain warrants issued in 2018 were recorded at their fair value on the date of issuance and are remeasured as of any warrant exercise date and at the end of each reporting period.

~~Interest expense, net~~

~~Interest expense, net, consists primarily of interest expense on our long-term debt facilities and non-cash interest related to the amortization of debt discount and issuance costs,~~ offset by interest earned on our cash equivalents.

Liquidity and Capital Resources

Overview

Since our inception in 2006, we have funded operations primarily through ~~June 30,~~proceeds from public issuances of common stock, our long-term debt and the private placement of our common stock.

As of March 31, 2020, we had approximately $26.5 million in cash and cash equivalents.

In April 2018, we entered into an amended and restated loan and security agreement with Hercules Capital, Inc. ("Hercules"), which was subsequently amended in November 2019 (as amended, the “2018 Term Loan”). The 2018 Term Loan provides a $14.0 million term loan. The 2018 Term Loan will mature on May 1, 2021 and accrues interest at a floating rate per annum equal to the greater of (i) 8.00% or (ii) the sum of 3.00% plus the prime rate. The 2018 Term Loan provides for interest-only payments until January

1, 2021. Thereafter, payments will include equal installments of principal and interest through maturity. The 2018 Term Loan may be prepaid subject to a prepayment charge. We are also obligated to pay an end of term charge of $1.0 million at maturity. As of March 31, 2020, the Company had outstanding borrowings of $13.5 million.

In October 2019, we entered into a purchase agreement with LPC pursuant to which LPC purchased $2.5 million of shares of our common stock at a purchase price of $2.587 per share. In addition, for a period of 30 months, we have the right, at our sole discretion, to sell up to an additional $27.5 million of our common stock based on prevailing market prices of our common stock at the time of each sale. In consideration for entering into the purchase agreement, we issued 289,966 shares of our common stock to LPC as a commitment fee. The purchase agreement limits our sales of shares of common stock to LPC to 5,227,323 shares of common stock, representing 19.99% of the shares of common stock outstanding on the date of the purchase agreement. The purchase agreement also prohibits us from directing LPC to purchase any shares of common stock if those shares, when aggregated with all other shares of our common stock then beneficially owned by LPC and its affiliates, would result in LPC and its affiliates having beneficial ownership, at any single point in time, of more than 9.99% of the then total outstanding shares of our common stock. In January 2020, the Company sold 186,986 shares of common stock to LPC, for net proceeds of approximately $0.4 million.

In June 2019, we entered into an underwriting agreement relating to the underwritten public offering of 10,500,000 shares of our common stock, par value $0.001 per share, at a price to the public of $3.50 per share, for gross proceeds of approximately $36.8 million (the “2019 Public Offering”). We also granted the underwriters an option to purchase up to an additional 1,575,000 shares of common stock (“Overallotment Option”). In June 2019, the underwriters exercised this option in full. We received ~~an aggregate of $396.8~~approximately $5.5 million in gross proceeds from the ~~issuance~~underwriter’s exercise of ~~equity securities and gross~~the Overallotment Option. In connection with the 2019 Public Offering, inclusive of the Overallotment Option, we incurred approximately $3.9 million of offering-related expenses, resulting in total net proceeds ~~from debt facilities and an aggregate~~ of ~~$7.9 million from grants. At June 30, 2019, our cash and cash equivalents were $58.7~~$38.4 million.

~~There have been no sales under our ATM during fiscal year 2019.~~In February 2019, we completed a private placement financing transaction (the “Private Placement”). We issued 3,199,998 shares (the “Shares”) of common stock, prefunded warrants (the “Pre-Funded Warrants”) to purchase 531,250 shares of common stock (the “Pre-Funded Warrant Shares”), and warrants (the “Private Placement Warrants”) to purchase up to 932,812 shares of common stock (the “Warrant Shares”). The Shares, Pre-Funded Warrants and Private Placement Warrants (collectively, the “Units”) were sold at a purchase price of $4.02 per Unit. We received net cash proceeds of approximately $13.8 million for the purchase of the Shares, Pre-Funded Warrant Shares and Warrant Shares.

Cash Flows

The following table summarizes our sources and uses of cash for the three months ended March 31, 2020 and 2019 (in thousands):



	Three Months Ended March 31,
	2020			2019
Net cash used in operating activities	$	(13,796	)	$	(10,299	)
Net cash used in investing activities	(217		)	(221		)
Net cash provided by financing activities	395			13,197
Net (decrease) increase in cash and cash equivalents	$	(13,618	)	$	2,677

Operating Activities

Net cash used in operating activities increased $3.5 million for the three months ended March 31, 2020 compared to the three months ended March 31, 2019. The cash used in operations for the three months ended March 31, 2020 was primarily related to the development of our preclinical and clinical candidates.

Investing activities

Net cash used by investing activities was for the purchases of property and equipment in both periods ending March 31, 2020 and 2019, respectively.

Financing Activities

Net cash provided by financing activities decreased $12.8 million for the three months ended March 31, 2020 compared to the three months ended March 31, 2019. In the three months ended March 31, 2020, the Company sold shares of common stock to

LPC, for net proceeds of approximately $0.4 million. In the three months ended March 31, 2019, the Private Placement generated net proceeds of $13.8 million.

Operating Capital Requirements

Our primary uses of capital are for compensation and related expenses, manufacturing costs for ~~pre-clinical~~preclinical and clinical materials, third-party clinical trial ~~research and development~~ services, laboratory and related supplies, ~~clinical costs,~~ legal and other regulatory expenses, and general overhead costs. We expect these costs will continue to be the primary operating capital requirements for the near future.

We expect that our existing cash and cash equivalents ~~as of June 30, 2019,~~ are sufficient to support our operations into the first quarter of 2021. WeAs reflected in the consolidated financial statements, we had available cash and cash equivalents of ~~$58.7~~$26.5 million at ~~June 30, 2019.~~March 31, 2020. In addition, we had ~~a loss from operations of $10.1 million and~~ cash used in operating activities of ~~$17.9~~$13.8 million for the ~~six~~three months ended ~~June 30, 2019.~~

March 31, 2020. These factors, combined with our forecast of cash required to fund operations for a period of at least one year from the date of issuance of these financial statements, raise substantial doubt about our ability to continue as a going concern. We have based our projections of operating capital requirements on assumptions that may prove to be incorrect and we may use all of our available capital resources sooner than we expect. Because of the numerous risks and uncertainties associated with research, development and commercialization of pharmaceutical products coupled with the global economic uncertainty that has arisen with the recent outbreak of the coronavirus, or referred to as COVID-19, we are unable to estimate the exact amount of our operating capital requirements. Our future funding requirements will depend on many factors, including, but not limited to:

the timing and costs of our planned clinical trials for GEN-009;

the progress, timing, and costs of manufacturing GEN-009 for planned clinical trials;

the outcome, timing, and costs of seeking regulatory approvals, including an IND application for GEN-011;

the initiation, progress, timing, costs, and results of preclinical studies and clinical trials for our other product candidates and potential product candidates;

the terms and timing of any future collaborations, grants, licensing, consulting, or other arrangements that we may establish;

the amount and timing of any payments we may be required to make, or that we may receive, in connection with the licensing, filing, prosecution, defense and enforcement of any patents or other intellectual property rights, including milestone payments, royalty payments and patent prosecution fees that we are obligated to pay pursuant to our license agreements;

the costs of preparing, filing, and prosecuting patent applications, maintaining and protecting our intellectual property rights, and defending against intellectual property related claims;

the extent to which we in-license or acquire other products and technologies;

the receipt of marketing approval;

the costs of commercialization activities for GEN-009 and other product candidates, if we receive marketing approval, including the costs and timing of establishing product sales, marketing, distribution, and manufacturing capabilities; and

revenue received from commercial sales of our product candidates.

We will need to obtain substantial additional funding in order to complete clinical trials and receive regulatory approval for GEN-009, GEN-011 and our other product candidates. To the extent that we raise additional capital through the sale of our common stock, convertible securities, or other equity securities, the ownership interests of our existing stockholders may be materially diluted and the terms of these securities could include liquidation or other preferences that could adversely affect the rights of our existing stockholders. In addition, debt financing, if available, would result in increased fixed payment obligations and may involve agreements that include restrictive covenants that limit our ability to take specific actions, such as incurring additional debt, making capital expenditures, or declaring dividends, that could adversely affect our ability to conduct our business. If we are unable to raise capital when needed or on attractive terms, we could be forced to significantly delay, scale back, or discontinue the development of GEN-009, GEN-011 or our other product candidates, seek collaborators at an earlier stage than otherwise would be desirable or on terms that are less favorable than might otherwise be available, and relinquish or license, potentially on unfavorable terms, our rights to GEN-009, GEN-011 or our other product candidates that we otherwise would seek to develop or commercialize ourselves.

~~Cash Flows~~

~~The following table summarizes our sources and uses of cash for each of the periods below (in thousands):~~

Six Months Ended June 30,
2019 2018
Net cash used in operating activities $ (17,942 ) $ (23,375 )
Net cash used in investing activities (635 ) (102 )
Net cash provided by financing activities 50,886
55,419
Net increase in cash and cash equivalents $ 32,309
$ 31,942

~~Operating Activities~~

Net cash used in operating activities decreased $5.4 million for the six months ended June 30, 2019 compared to the six months ended June 30, 2018. The decrease in net cash used was due primarily due to favorable changes in working capital attributable to accounts payable and accrued expenses.

~~Investing Activities~~

~~Net cash used in investing activities increased~~ ~~$0.5 million~~ ~~for the~~ ~~six months ended June 30, 2019~~ ~~compared to the~~ ~~six months endedJune 30, 2018. The increase in net cash used was primarily due to fixed asset additions.~~

~~Financing Activities~~

Net cash provided by financing activities decreased $4.5 million for the six months ended June 30, 2019 compared to the six months ended June 30, 2018. In the six months ended June 30, 2018, the 2018 Public Offering generated net proceeds of $51.7 million and shares of common stock issued pursuant to our ATM facility generated net proceeds of $2.9 million, whereas in the six months ended June 30, 2019, the Private Placement generated net proceeds of $13.8 million and the 2019 Public Offering generated net proceeds of $38.4 million.

Off-Balance Sheet Arrangements

We do not have any off-balance sheet arrangements.

Item 3. Quantitative and Qualitative Disclosures about Market ~~Risks~~Risk

We ~~are exposed to market risk related to changes in interest rates. As of June 30, 2019, we~~ had cash and cash equivalents of ~~$58.7~~approximately $26.5 million ~~consisting primarily~~as of ~~money market funds.~~March 31, 2020. The primary objectives of our investment activities are to preserve principal, provide liquidity and maximize income without significantly increasing risk. Our primary exposure to market risk isrelates to fluctuations in interest ~~rate sensitivity,~~rates, which isare affected by changes in the general level of U.S. interest rates. ~~Since~~Given the short-term nature of our ~~investments are limited to money market funds, an immediate 100 basis point~~cash and cash equivalents, we believe that a sudden change in market interest rates would not be expected to have a material impact on our financial condition and/or results of operations. We do not own any derivative financial instruments.

We do not believe that our cash, cash equivalents and marketable securities have significant risk of default or illiquidity. While we believe our cash and cash equivalents do not contain excessive risk, we cannot provide absolute assurance that in the future our investments will not be subject to adverse changes in market value. In addition, we maintain significant amounts of cash, cash equivalents and marketable securities at one or more financial institutions that are in excess of federally insured limits.

Inflation generally affects us by increasing our cost of labor and clinical trial costs. We do not believe that inflation had a material effect on our results of operations during the ~~fair market value of our portfolio.~~

We are also exposed to market risk related to change in foreign currency exchange rates. We contract with certain vendors that are located in Europe which have contracts denominated in foreign currencies. We are subject to fluctuations in foreign currency rates in connection with these agreements. We do not currently hedge our foreign exchange rate risk. As of June 30, 2019, we had minimal liabilities denominated in foreign currencies.three months ended March 31, 2020.

Item 4. Controls and Procedures

Management’s Evaluation of our Disclosure Controls and Procedures

We maintain disclosure controls and procedures that are designed to ensure that information required to be disclosed in the reports that we file or submit under the Securities Exchange Act of 1934, as amended, is (1) recorded, processed, summarized, and reported within the time periods specified in the SEC’s rules and forms and (2) accumulated and communicated to our management, including our principal executive officer and principal financial officer, to allow timely decisions regarding required disclosure.

Our management, with the participation of our principal executive officer and principal financial officer, evaluated the effectiveness of our disclosure controls and procedures as of ~~June 30, 2019~~March 31, 2020 (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended). Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives, and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Our principal executive officer and principal financial officer have concluded based upon the evaluation described above that, as of ~~June 30, 2019,~~March 31, 2020, our disclosure controls and procedures were effective at the reasonable assurance level.

Changes in Internal Control Over Financial Reporting

During the ~~six~~three months ended ~~June 30, 2019,~~March 31, 2020, there have been no changes in our internal control over financial reporting, as such term is defined in Rules 13a-15(f) and 15(d)-15(f) promulgated under the Securities Exchange Act of 1934, as amended, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

PART II. OTHER INFORMATION

Item 1. Legal Proceedings

In the ordinary course of business, we are from time to time involved in lawsuits, claims, investigations, proceedings, and threats of litigation relating to intellectual property, commercial arrangements and other matters. ~~Except as discussed below, we~~We do not believe we are currently party to any pending legal action, arbitration proceeding or governmental proceeding, the outcome of which, if determined adversely to us, would individually or in the aggregate be reasonably expected to have a material adverse effect on our business or operating results. We are not a party to any material proceedings in which any director, member of senior management or affiliate of ours is either a party adverse to us or our subsidiaries or has a material interest adverse to us or our subsidiaries.

~~Pending Litigation:~~

~~Emerson v. Genocea Biosciences et al., U.S. District Court (Mass.), Civil Action No. 17-cv-12137-PBS (the “Emerson~~ Action”). In 2017, three purported shareholders filed placeholder complaints against Genocea and certain of its officers alleging violations of the federal securities laws in connection with the Company’s disclosures related to GEN-003, a Phase 3-ready investigational immunotherapy for the treatment of genital herpes infections. On February 12, 2018, the Court appointed the Genocea Investor Group (a group of five purported shareholders) as lead plaintiff in the consolidated proposed class action, and appointed Scott+Scott LLP, Levi & Korsinsky LLP, and Block & Leviton LLP as lead counsel. The lead plaintiff filed an amended complaint on March 29, 2018. Defendants filed a motion to dismiss on May 14, 2018. The lead plaintiff filed an opposition to defendants’ motion to dismiss on June 28, 2018, as well as a motion to strike certain documents attached to defendants’ motion to dismiss, on June 29, 2018. Defendants filed a reply in further support of the dismissal motion, and an opposition to plaintiffs’ motion to strike, on July 30, 2018. The court held oral argument on the motion to dismiss and motion to strike on September 25, 2018. On December 6, 2018, the court granted defendants’ motion to dismiss and, because the court’s decision did not consider the documents plaintiffs sought to strike, did not rule on plaintiffs’ motion to strike. On January 7, 2019, plaintiffs filed a notice of appeal in the District of Massachusetts to appeal the court’s order granting defendants’ motion to dismiss. The appeal, captioned ~~Yuksel v. Genocea Biosciences, Inc., et al.~~, U.S. Court of Appeal for the First Circuit, Case No. 19-1036, was docketed in the First Circuit on January 15, 2019. By order dated January 29, 2019, the First Circuit set a deadline of March 11, 2019 for plaintiffs’ opening brief. Shortly thereafter, however, plaintiffs made a settlement offer to defendants, and the parties subsequently entered into a settlement agreement and general release on April 22, 2019. In connection with the settlement agreement, the parties fully and finally resolved the ~~Emerson~~ Action, including the entry of a general release, and plaintiffs agreed to request a voluntary dismissal of the appeal with prejudice pursuant to Federal Rule of Appellate Procedure 42(b). On May 9, 2019, plaintiffs filed the voluntarily dismissal motion. The Court dismissed the ~~Emerson~~ ~~Action on May 23, 2019.~~

~~Proxy Statement, filed with the SEC on April 21, 2017. The complaint also alleged claims for breach of fiduciary duty, unjust enrichment, and waste of corporate assets. As detailed above, the~~ ~~Howard~~ ~~action was consolidated with the~~ ~~Kahr~~ ~~action into the Genocea Consolidated Derivative Action, which the court stayed until,~~ ~~inter alia, the resolution of the First Circuit appeal in the~~ ~~Emerson~~ ~~Action. Following the dismissal of the~~ ~~Emerson~~ ~~action, however, the plaintiff from the~~ ~~Kahr~~ ~~action voluntarily dismissed the Genocea Consolidated Derivative Action on July 1, 2019. The court closed the~~ ~~Howard~~ ~~action on July 1, 2019.~~

~~The Company does not have contingency reserves established for any litigation liabilities.~~

Item 1A. Risk Factors

There have been no material changes from the risk factors set forth in the Company's Annual Report Form 10-K for the year ended December 31, ~~2018.~~2019, except as set forth below.

A pandemic, epidemic or outbreak of an infectious disease, such as the novel coronavirus, or COVID-19, has and may in the future adversely affect our business.

~~Item 5. Other Information.~~

An outbreak of COVID-19 occurred in China in December 2019 and has spread around the world. The Center for Disease Control (CDC) has recognized this outbreak as a pandemic which has caused shutdowns to businesses and cities worldwide while disrupting supply chains, business operations, travel, consumer confidence, and business sentiment. The situation is ever evolving and its effects both short-term and long-term remain unknown. The spread of COVID-19 has resulted in certain disruptions to our business and may result in future additional disruptions to our business. Examples of both include without limitation the following:


•	The COVID-19 pandemic has materially affected our ability to conduct research, principally to explore Inhibigen^TM biology and ways to further strengthen ATLAS and other program opportunities.

The ~~following disclosure~~health and wellbeing of our employees and suppliers is ~~provided~~at risk- if a critical threshold of our personnel, or the personnel of our suppliers, were to be diagnosed with COVID-19, placed in ~~accordance~~quarantine due to potential exposure to COVID-19, or need to care for family members diagnosed with COVID-19, it may result in significant manufacturing and business disruption.

Our clinical sites may no longer be able to continue with the GEN-009 clinical trial or limit patient enrollment which could have a material impact on our milestones and timelines. Further, clinical sites may not be engaging in ~~satisfaction~~new clinical programs which could have a material impact on our GEN-011 program.

We have asked most employees who are not directly involved in our GEN-009 and GEN-011 clinical programs to work from home, which could impact our ability to effectively plan, execute, communicate and maintain our corporate culture. The increase in working remotely could increase our cyber security risk, create data accessibility concerns, and make us more susceptible to communication disruptions, any of which could adversely impact our business operations.

Stay at home orders have significantly limited the ability of individuals from traveling outside the home which may limit our ability to hire new employees or backfill terminated employees.

Equity and debt markets have experienced significant volatility since the spread of COVID-19 into the United States. Should significant volatility continue or they experience declines due to the economic impact of COVID-19, we may not be able to raise capital at a reasonable valuation or at all.

The full extent to which COVID-19 impacts our business will depend on future developments, which are highly uncertain and cannot be predicted, including new information which may emerge concerning the severity of COVID-19 and the actions to treat or contain COVID-19 or to otherwise limit its impact, among others.

Disruptions at the FDA and other government agencies caused by funding shortages or global health concerns could hinder their ability to hire, retain or deploy key leadership and other personnel, or otherwise prevent new or modified products from being developed, cleared or approved, or commercialized in a timely manner or at all, which could negatively impact our business.

The ability of the ~~requirements~~FDA to review and clear or approve new products can be affected by a variety of ~~Item 2.02 “Results~~factors, including government budget and funding levels, statutory, regulatory, and policy changes, the FDA’s ability to hire and retain key personnel and accept the payment of ~~Operations~~user fees, and ~~Financial Condition~~”other events that may otherwise affect the FDA’s ability to perform routine functions. Average review times at the agency have fluctuated in recent years as a result. In addition, government funding of ~~Form 8-K:~~other government agencies that fund research and development activities is subject to the political process, which is inherently fluid and unpredictable. Disruptions

~~On July 25, 2019, Genocea~~

at the FDA and other agencies may also slow the time necessary for marketing applications, clinical trial authorizations or other regulatory submissions to drug candidates to be reviewed and/or approved by necessary government agencies, which would adversely affect our business. For example, over the last several years, including for 35 days beginning on December 22, 2018, the U.S. government has shut down several times and certain regulatory agencies, such as the FDA, have had to furlough critical employees and stop critical activities.

Separately, in response to the global pandemic of COVID-19, on March 10, 2020, the FDA announced its ~~financial results for~~intention to postpone most foreign inspections of manufacturing facilities and products through April 2020, and subsequently, on March 18, 2020, the ~~quarter ended June 30, 2019 and commented on certain corporate accomplishments and plans. The full text~~FDA announced its intention to temporarily postpone routine surveillance inspections of domestic manufacturing facilities. Regulatory authorities outside the United States may adopt similar restrictions or other policy measures in response to the COVID-19 pandemic. If a prolonged government shutdown occurs, or if global health concerns continue to prevent the FDA or other regulatory authorities from conducting their regular inspections, reviews, or other regulatory activities, it could significantly impact the ability of the ~~press release issued in connection with the announcement is furnished as Exhibit 99.1 hereto.~~

~~The following disclosure is provided in accordance with~~FDA or other regulatory authorities to timely review and ~~in satisfaction of the requirement of Item 5.02~~ ~~“Departure of Directors~~process our marketing applications, clinical trial authorizations, or ~~Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers”~~ ~~of Form 8-K:~~

~~On July 22, 2019, Pamela Carroll resigned as Senior Vice President, Immuno-oncology, effective August 13, 2019 (“Separation Date”), to pursue~~ other ~~professional opportunities. The Company and Ms. Carroll entered into~~regulatory submissions, which could have a Separation Agreement (the “Separation Agreement”) in connection with the termination of Ms. Carroll’s employment with the Company. Pursuant to the Separation Agreement, Ms. Carroll will receive the following benefits: (i) cash payment of her monthly base salary for 6 months, and (ii) payment of monthly COBRA premiums until the earlier of the conclusion of 6 months following the Separation Date or the date that she is no longer eligible for COBRA or Company benefit plans. Additionally, all unvested stock options granted by the Company to Ms. Carroll prior to the Separation Date, which are outstanding as of the Separation Date, and vest only basedmaterial adverse effect on the passage of time, by their terms, and which would have vested during the six (6) month period immediately following the Separation Date, shall, notwithstanding the terms of the equity compensation plans and award agreements to which such stock options are subject, automatically become fully vested as of the date of the Separation Agreement. our business.

Item 6. Exhibits



Exhibit Number		Exhibit
~~3.1~~10.1*		~~Certificate of Amendment to Restated Certificate of Incorporation of~~Employment Letter Agreement between Girish Aakalu and Genocea Biosciences, Inc. ~~(incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, File No. 001-36289, filed on May 21, 2019)~~, dated December 6, 2018

10.110.2		~~Separation~~Employment Letter Agreement ~~dated July 22, 2019~~ between Thomas Davis and Genocea Biosciences, Inc. ~~and Pamela Carroll~~, dated October 1, 2018

10.3*†		Form of Restricted Stock Unit Award Agreement under the Genocea Biosciences, Inc. 2014 Equity Incentive Plan

31.1		Certification pursuant to Section 302 of Sarbanes Oxley Act of 2002 by Chief Executive Officer

31.2		Certification pursuant to Section 302 of Sarbanes Oxley Act of 2002 by Chief Financial Officer

32.1		Certification of periodic financial report pursuant to Section 906 of Sarbanes Oxley Act of 2002 by Chief Executive Officer

32.2		Certification of periodic financial report pursuant to Section 906 of Sarbanes Oxley Act of 2002 by Chief Financial Officer

101		The following materials from the Company’s Quarterly Report on Form 10-Q for the quarter ended ~~June 30, 2019,~~March 31, 2020, formatted in XBRL (eXtensible Business Reporting Language): (i) Condensed Consolidated Balance Sheets as of ~~June 30, 2019~~March 31, 2020 and December 31, ~~2018,~~2019, (ii) Condensed Consolidated Statements of Operations and Comprehensive Income for the three ~~and six~~ months ended ~~June 30,~~March 31, 2020 and 2019, ~~and 2018,~~ (iii) Condensed Consolidated Statements of Stockholders' Equity (Deficit) for the ~~six~~three months ended ~~June 30,~~March 31, 2020 and 2019, ~~and 2018,~~ (iv) Condensed Consolidated Statements of Cash Flows for the ~~six~~three months ended ~~June 30,~~March 31, 2020 and 2019 ~~and 2018~~ and (v) Notes to Unaudited Condensed Consolidated Financial Statements

* Filed herewith.

† Indicates a compensatory plan.

SIGNATURES

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



	Genocea Biosciences, Inc.

Date: ~~July 25, 2019~~April 30, 2020	By:	/s/ WILLIAM D. CLARK
		William D. Clark
		President and Chief Executive Officer and Director
		(Principal Executive Officer)

Date: ~~July 25, 2019~~April 30, 2020	By:	/s/ DIANTHA DUVALL
		Diantha Duvall
		Chief Financial Officer
		(Principal Financial and Accounting Officer)

3027



	Shares		Weighted- Average Exercise Price		Weighted- Average Remaining Contractual Term (years)	Aggregate Intrinsic Value
Outstanding at December 31, 2018	893		$	18.79		$	—
Granted	501		$	4.66
Exercised	(5	)	$	4.32
Cancelled	(104	)	$	25.24
Outstanding at June 30, 2019	1,285		$	12.81	8.32	$	1,435
Exercisable at June 30, 2019	402		$	25.57	6.38	$	—

March 31, 2020

March 31, 2019

Weighted average remaining lease term in years

Weighted average discount rate