~~Delaware~~		~~04‑3562403~~


Delaware	04-3562403
(State or other jurisdiction of		~~(I.R.S. Employer~~
incorporation or organization)		(I.R.S. Employer Identification No.)


Title of each class	Trading symbol(s)	Name of each exchange on which registered
Common Stock, $0.0001 par value	MRSN	The Nasdaq Global Select Market

Large accelerated filer

☐

Accelerated filer

☒

Non-accelerated filer

☐

Smaller reporting company

☒

Emerging growth company

☒

There were ~~58,949,470~~68,497,425 shares of Common Stock ($0.0001 par value per share) outstanding as of ~~May 5,~~November 4, 2020.

Unless otherwise stated or the context requires otherwise, all references to “us,” “our,” “we,” the “Company” and similar designations in this Quarterly Report on Form 10-Q refer to Mersana Therapeutics, Inc. and its consolidated subsidiary, Mersana Securities Corp.

FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q contains ~~forward‑looking~~forward-looking statements. ~~Forward‑looking~~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 “aim,” “anticipate,” “believe,” “contemplate,” “continue,” “could,” “estimate,” “expect,” “goal,” “intend,” “may,” “on track,” “plan,” “possible,” “potential,” “predict,” “project,” “seek,” “should,” “target,” “will,” “would” or the negative of these terms or other similar expressions are intended to identify ~~forward‑looking~~forward-looking statements, although not all ~~forward‑looking~~forward-looking statements contain these identifying words.

These ~~forward‑looking~~forward-looking statements include, among other things, statements about:

~~the initiation, cost, timing, progress and results of our current and future research and development activities and preclinical and clinical studies;~~

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

•the initiation, cost, timing, progress and results of our current and future research and development activities and preclinical and clinical studies;

~~unmet need of ovarian cancer and non-small cell lung cancer;~~

•the adequacy of our inventory of XMT-1536 and XMT-1592 to support our ongoing clinical studies, as well as the outcome of planned manufacturing runs;

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

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

~~our ability to advance any product candidate into, and successfully complete clinical studies;~~

•unmet need of ovarian cancer and non-small cell lung cancer;

~~our intellectual property position, including with respect to our trade secrets;~~

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

~~the potential benefits of strategic partnership agreements and our ability to enter into selective strategic partnerships;~~

•our ability to advance any product candidate into, and successfully complete, clinical studies;

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

•our intellectual property position, including with respect to our trade secrets;

~~the potential impact of the ongoing COVID-19 pandemic~~.

•the potential benefits of strategic partnership agreements and our ability to enter into selective strategic partnerships;

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

•the potential impact of the ongoing COVID-19 pandemic.

We may not actually achieve the plans, intentions or expectations disclosed in our ~~forward‑looking~~forward-looking statements, and you should not place undue reliance on our ~~forward‑looking~~forward-looking statements. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the ~~forward‑looking~~forward-looking statements we make. We have included important factors in the cautionary statements included in our Annual Report on Form 10-K for the year ended December 31, 2019 and ~~in this~~our Quarterly Report on Form 10-Q for the quarterly period ended March 31, 2020, particularly in the “Risk Factors” sections, that we believe could cause actual results or events to differ materially from the ~~forward‑looking~~forward-looking statements that we make. Our ~~forward‑looking~~forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, joint ventures or investments we may make.

In addition, while we expect that the COVID-19 pandemic might adversely affect our preclinical and clinical development efforts, business operations and financial results, the extent of the impact and the value of and market for our common stock will depend on future developments that are highly uncertain and cannot be predicted with confidence at this time, such as the ultimate duration of the pandemic, travel restrictions, quarantines, physical distancing and business closure requirements in the U.S. and in other countries, and the effectiveness of actions taken globally to contain and treat the disease.

The ~~forward‑looking~~forward-looking statements contained herein represent our views as of the date of this Quarterly Report on Form 10-Q. We anticipate that subsequent events and developments will cause our views to change. You should, therefore, not rely on these ~~forward‑looking~~forward-looking statements as representing our views as of any date subsequent to the date of this Quarterly Report on Form 10-Q.

Table of Contents

TABLE OF CONTENTS


			Page
PART I – FINANCIAL INFORMATION
Item 1. Financial Statements (unaudited)
Condensed Consolidated Balance Sheets as of ~~March 31,~~September 30, 2020 and December 31, 2019			4 4
Condensed Consolidated Statements of Operations and Comprehensive ~~Income (Loss)~~Loss for the three and nine months ended ~~March 31,~~September 30, 2020 and 2019			5 5
Condensed Consolidated Statement of Stockholders’ Equity for the three and nine months ended ~~March 31,~~September 30, 2020 and 2019			6 6
Condensed Consolidated Statements of Cash Flows for the ~~three~~nine months ended ~~March 31,~~September 30, 2020 and 2019			7 7
Notes to Condensed Consolidated Financial Statements			8 8
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations			23 23
Item 3. Quantitative and Qualitative Disclosures About Market Risk			34 31
Item 4. Controls and Procedures			34 32
PART II - OTHER INFORMATION			36 33
Item 1. Legal Proceedings			36 33
Item 1A. Risk Factors			36 33
Item 6. Exhibits			36 35
Signatures			37 36

Table of Contents

PART I – FINANCIAL INFORMATION

Item 1. Financial Statements

Mersana Therapeutics, Inc.

Condensed Consolidated Balance Sheets

(in thousands, except share and per share data)

(unaudited)


	March 31,		December 31,
	2020		2019			September 30, 2020		December 31, 2019
Assets					Assets
Current assets:					Current assets:
Cash and cash equivalents	$	60,450	$	62,351	Cash and cash equivalents	$	270,936	$	62,351
Short-term marketable securities		17,976		37,439	Short-term marketable securities	0		37,439

Prepaid expenses and other current assets		1,866		1,536	Prepaid expenses and other current assets	3,998		1,536
Total current assets		80,292		101,326	Total current assets	274,934		101,326
Property and equipment, net		1,979		2,164	Property and equipment, net	1,698		2,164
Operating lease right-of-use assets		12,134		2,598	Operating lease right-of-use assets	11,343		2,598
Other assets		1,453		1,453	Other assets	2,153		1,453
Total assets	$	95,858	$	107,541	Total assets	$	290,128	$	107,541
Liabilities and stockholders’ equity					Liabilities and stockholders’ equity
Current liabilities:					Current liabilities:
Accounts payable	$	4,603	$	7,296	Accounts payable	$	4,528	$	7,296
Accrued expenses		5,678		8,986	Accrued expenses	11,173		8,986
Deferred revenue		4,804		4,815	Deferred revenue	3,998		4,815
Operating lease liabilities		1,150		2,219	Operating lease liabilities	1,280		2,219
Short-term debt		1,167		667	Short-term debt	0		667
Other liabilities		88		87	Other liabilities	91		87
Total current liabilities		17,490		24,070	Total current liabilities	21,070		24,070
Operating lease liabilities		11,295		677	Operating lease liabilities	10,606		677
Long-term debt, net		3,732		4,201	Long-term debt, net	4,944		4,201
Other liabilities		250		275	Other liabilities	200		275
Total liabilities		32,767		29,223	Total liabilities	36,820		29,223
Commitments (Note 12)
Commitments (Note 11)					Commitments (Note 11)
Stockholders' equity:					Stockholders' equity:
Preferred stock, $0.0001 par value; 25,000,000 shares authorized; 0 shares issued and outstanding at March 31, 2020 and December 31, 2019, respectively		—		—
Common stock, $0.0001 par value; 175,000,000 shares authorized; 48,006,049 and 45,388,023 shares issued and outstanding at March 31, 2020 and December 31, 2019, respectively		5		5
Preferred stock, $0.0001 par value; 25,000,000 shares authorized; 0 shares issued and outstanding at September 30, 2020 and December 31, 2019, respectively					Preferred stock, $0.0001 par value; 25,000,000 shares authorized; 0 shares issued and outstanding at September 30, 2020 and December 31, 2019, respectively	0		0
Common stock,$0.0001 par value; 175,000,000 shares authorized; 68,470,081 and 45,388,023 shares issued and outstanding at September 30, 2020 and December 31, 2019, respectively					Common stock,$0.0001 par value; 175,000,000 shares authorized; 68,470,081 and 45,388,023 shares issued and outstanding at September 30, 2020 and December 31, 2019, respectively	7		5
Additional paid-in capital		272,390		270,662	Additional paid-in capital	504,876		270,662
Accumulated other comprehensive income (loss)		(4)		25	Accumulated other comprehensive income (loss)	0		25
Accumulated deficit		(209,300)		(192,374)	Accumulated deficit	(251,575)		(192,374)
Total stockholders’ equity		63,091		78,318	Total stockholders’ equity	253,308		78,318
Total liabilities and stockholders’ equity	$	95,858	$	107,541	Total liabilities and stockholders’ equity	$	290,128	$	107,541

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements

(in thousands, except share and per share data)

(unaudited)

1. Nature of business and basis of ~~presentation~~

presentation

Mersana Therapeutics, Inc. is a clinical stage biopharmaceutical company focused on developing antibody drug conjugates (ADCs) that offer a clinically meaningful benefit for cancer patients with significant unmet need. The Company has leveraged 20 years of industry learning in the ADC field to develop proprietary and differentiated technology platforms that enable it to design ADCs to have improved efficacy, safety and tolerability relative to existing ADC therapies. The Company’s innovative platforms, which include Dolaflexin and Dolasynthen, each delivering its DolaLock payload, as well as Immunosynthen, delivering a novel stimulator of interferon genes (STING) agonist, provide an efficient product engine that has enabled a robust discovery pipeline for the Company and its partners. The Company’s product candidates include ~~XMT‑1536~~XMT-1536 and XMT-1592. The Company's early stage programs include a potentially first-in-class B7-H4-targeted DolaLock ADC as well as candidates leveraging the Immunosynthen platform.

XMT-1536, an ADC utilizing the Company’s Dolaflexin platform and targeting NaPi2b, an antigen broadly expressed in ovarian cancer and non-small cell lung cancer (NSCLC) adenocarcinoma, is currently in the expansion portion of a Phase 1 study in patients with ovarian cancer and NSCLC adenocarcinoma. XMT-1592 uses one of the Company’s new platforms, Dolasynthen, and also targets NaPi2b. The Company filed an Investigational New Drug (IND) application in the first quarter of 2020 ~~which was approved by the U.S. Food~~ and ~~Drug Administration (FDA). The Company remains on track to initiate~~initiated the Phase 1 dose escalation study of XMT-1592 in the second quarter of 2020.

The Company has incurred cumulative net losses since inception. For the ~~three~~nine months ended ~~March 31,~~September 30, 2020, the net loss was ~~$16,926,~~$59,203, compared to net ~~income~~loss of ~~$21,901~~$11,962 in the ~~three~~nine months ended ~~March 31,~~September 30, 2019. The difference year over year is primarily attributable to $39,965 in deferred revenue that was recognized in the first quarter of 2019 as a result of the discontinuation of the partnership with Takeda in ~~the first quarter of 2019.~~that quarter. The Company expects to continue to incur operating losses for at least the next several years. As of ~~March 31,~~September 30, 2020, the Company had an accumulated deficit of $~~209,300~~.$251,575. The future success of the Company is dependent on, among other factors, its ability to identify and develop its product candidates and ultimately upon its ability to attain profitable operations. The Company has devoted substantially all of its financial resources and efforts to research and development and general and administrative expense to support such research and development. Net losses and negative operating cash flows have had, and will continue to have, an adverse effect on the Company’s stockholders' equity and working capital.

In April 7, 2020, the Company sold ~~8,938,599 and 1,962,000~~10,900,599 shares of common stock ~~at $5.59 per share~~ and ~~$7.74 per share, respectively, to raise gross~~received net proceeds of ~~$65,153 through its at-the-market equity offering program (ATM).~~$62,976. In addition, in June 2020, the Company sold 9,200,000 shares of common stock and received net proceeds of $163,991. The Company believes that its currently available funds will be sufficient to fund the Company’s operations through at least the next twelve months from the issuance of this Quarterly Report on Form 10-Q. Management’s belief with respect to its ability to fund operations is based on estimates that are subject to risks and uncertainties. If actual results are different from management’s estimates, the Company may need to seek additional funding.

The Company is subject to risks common to companies in the biotechnology industry, including but not limited to, the need for additional capital, risks of failure of preclinical and clinical studies, the need to obtain marketing approval and reimbursement for any drug product candidate that it may identify and develop, the need to successfully commercialize and gain market acceptance of its product candidates, dependence on key personnel, protection of proprietary technology, compliance with government regulations, development of technological innovations by competitors, reliance on third party manufacturers and the ability to transition from pilot-scale production to large-scale manufacturing of products.

The Company’s unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States (U.S. GAAP) and the rules and regulations of the Securities and Exchange Commission (SEC). Any reference in these notes to applicable guidance is meant to refer to the authoritative ~~United States generally accepted accounting principles~~U.S. GAAP as found in the Accounting Standards Codification (ASC) and Accounting Standards

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

Updates (ASU) of the Financial Accounting Standards Board (FASB). All dollar amounts, except per share data in the text and tables herein, are stated in thousands unless otherwise indicated. Certain information and footnote disclosures normally included in annual financial statements prepared in accordance with U.S. GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations. Accordingly, these financial statements should be read in conjunction with the audited financial statements as of and for the year

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~~Mersana Therapeutics, Inc.~~

~~Notes to condensed consolidated financial statements (continued)~~

~~(in thousands, except share and per share data)~~

~~(unaudited)~~

ended December 31, 2019 and the notes thereto, included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2019 filed with the SEC on February 28, 2020.

The unaudited condensed consolidated financial statements have been prepared on the same basis as the audited financial statements. In the opinion of the Company’s management, the accompanying unaudited condensed consolidated financial statements contain all adjustments that are necessary to present fairly the Company’s financial position as of ~~March 31,~~September 30, 2020, the results of its operations for the three and nine months ended ~~March 31,~~September 30, 2020 and 2019, a statement of stockholders’ equity for the three and nine months ended ~~March 31,~~September 30, 2020 and 2019 and cash flows for the ~~three~~nine months ended ~~March 31,~~September 30, 2020 and 2019. Such adjustments are of a normal and recurring nature. The results for the three and nine months ended ~~March 31,~~September 30, 2020 are not necessarily indicative of the results for the year ending December 31, 2020, or for any future period.

2. Summary of Significant Accounting Policies

Principles of Consolidation

The accompanying unaudited condensed consolidated financial statements include those of the Company and its ~~wholly-owned~~wholly owned subsidiary, Mersana Securities Corp. All intercompany balances and transactions have been eliminated.

The preparation of the Company’s unaudited condensed consolidated financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, equity, revenue, expenses and related disclosure of contingent assets and liabilities at the date of the financial statements and reported amounts of revenue and expenses during the reporting period. On an ongoing basis, the Company’s management evaluates its estimates which include, but are not limited to, management’s judgments with respect to the identification of performance obligations and standalone selling prices of those performance obligations within its revenue arrangements, accrued expenses, valuation of stock-based awards and income taxes. Actual results could differ from those estimates.

Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision-maker, or decision making group, in deciding how to allocate resources and assess performance. The Company views its operations and manages its business as a single operating segment, which is the business of discovering and developing ADCs.

Summary of Accounting Policies

The significant accounting policies used in preparation of these condensed consolidated financial statements for the three and nine months ended ~~March 31,~~September 30, 2020 are consistent with those discussed in Note 2 to the consolidated financial statements in the Company’s 2019 Annual Report on Form ~~10-K.~~

10-K, except as otherwise noted below in "Recently Issued Accounting Pronouncements."

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

Fair Value Measurements

Fair value is defined as the price that would be received upon sale of an asset or paid to transfer a liability between market participants at measurement dates. ASC Topic 820 Fair Value Measurement (ASC 820) establishes a three-level valuation hierarchy for instruments measured at fair value. The hierarchy is based on the transparency of inputs to the valuation of an asset or liability as of the measurement date. The three levels are defined as follows:

Level 1—Inputs to the valuation methodology are quoted prices (unadjusted) for identical assets or liabilities in active markets.

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~~Mersana Therapeutics, Inc.~~

~~Notes to condensed consolidated financial statements (continued)~~

~~(in thousands, except share and per share data)~~

~~(unaudited)~~

Level 2—Inputs to the valuation methodology include quoted prices for similar assets and liabilities in active markets, and inputs that are observable for the asset or liability, either directly or indirectly, for substantially the full term of the financial instrument.

Level 3—Inputs to the valuation methodology are unobservable and significant to the fair value measurement.

Cash and Cash Equivalents

The Company considers all ~~highly-liquid~~highly liquid investments with an original maturity, or a remaining maturity at the time of purchase, of three months or less to be cash equivalents. The Company invests excess cash primarily in money market funds, commercial paper and government agency securities, which are highly liquid and have strong credit ratings. These investments are subject to minimal credit and market risks. Cash and cash equivalents are stated at cost, which approximates market value.

Marketable Securities

Short-term marketable securities consist of investments in debt securities with maturities greater than three months and less than one year from the balance sheet date. The Company classifies all of its marketable securities as available-for-sale. Accordingly, these investments are recorded at fair value. Amortization and accretion of discounts and premiums are recorded as interest income within other income. ~~Unrealized~~Prior to the adoption of ASU 2016-13, Financial Instruments - Credit Losses, unrealized gains and losses on available-for-sale securities are included in other accumulated comprehensive income (loss) as a component of stockholders’ equity until realized. Realized gains and losses and declines in value judged to be other than temporary are included as a component of other income (expense), net, based on the specific identification method. When determining whether a decline in value is other than temporary, the Company considers various factors, including whether the Company has the intent to sell the security, and whether it is more likely than not that the Company will be required to sell the security prior to recovery of its amortized cost basis. Fair value is determined based on quoted market prices.

The Company recorded other assets of $2,153 and $1,453 as of ~~March 31,~~September 30, 2020 and December 31, 2019, respectively, comprised of $1,832 and $1,132, respectively, held by a service provider, and restricted cash of $321 at the end of each period held as security deposits for a standby letter of credit related to a facility ~~lease~~lease.

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and ~~$1,132 held by a service provider.~~

per share data)

(unaudited)

Basic net loss per common share is calculated by dividing the net loss attributable to common stockholders by the weighted-average number of shares of common stock outstanding during the period, without further consideration for potentially dilutive securities. Diluted net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted-average number of shares of common stock and potentially dilutive securities outstanding for the period determined using the treasury stock and if-converted methods.

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~~Mersana Therapeutics, Inc.~~

~~Notes to condensed consolidated financial statements (continued)~~

~~(in thousands, except share and per share data)~~

~~(unaudited)~~

For purposes of the diluted net loss per share calculation, stock options, unvested restricted stock units (RSUs) ~~and~~, warrants to purchase common stock and options to purchase common stock are considered to be potentially dilutive securities, but are excluded from the calculation of diluted net loss per share because their effect would be ~~anti-dilutive. Therefore,~~anti-dilutive and therefore, basic and diluted net loss per share were the same for ~~the three months ended March 31, 2020.~~

all periods presented.

The following table sets forth the outstanding potentially dilutive securities that have been excluded from the calculation of diluted net loss per share for the ~~period~~three and nine months ended ~~March 31,~~September 30, 2020 and 2019, because to include them would be anti-dilutive (in common stock equivalent shares):


		~~Three months ended~~
		~~March 31,~~
		~~2020~~
~~Stock options~~		~~6,049,288~~
~~Restricted stock units~~		~~760,193~~
~~Warrants~~		~~39,474~~
		~~6,848,955~~


	Three and Nine Months Ended September 30, 2020	Three and Nine Months Ended September 30, 2019
Stock options	6,215,368		4,718,597
Unvested restricted stock units	740,862		447,336
Warrants	39,474		39,474
	6,995,704		5,205,407

Recently Issued Accounting Pronouncements

In November 2018, the FASB issued ASU No. 2018-18, Collaborative Arrangements (Topic 808):Clarifying the Interaction between Topic 808 and Topic 606. The main provisions of ASU 2018-18 include: (i) clarifying that certain transactions between collaborative arrangement participants should be accounted for as revenue when the collaborative arrangement participant is a customer in the context of a unit of account and (ii) precluding the presentation of transactions with collaborative arrangement participants that are not directly related to sales to third parties together with revenue. This guidance is effective for annual reporting periods beginning after December 15, 2019, including interim periods within those annual reporting periods, and early adoption is permitted. The guidance per ASU 2018-18 is to be adopted retrospectively to the date of initial application of Topic 606. The Company adopted the new standard effective January 1, 2020. The adoption of this standard did not have a material impact on the Company’s consolidated financial statements and related disclosures.

In June 2016, the FASB issued ASU 2016-13, Financial Instruments-Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments, which requires that financial assets measured at amortized cost be presented at the net amount expected to be collected. ~~Currently,~~Historically, U.S. GAAP ~~delays~~delayed recognition of the full amount of credit losses until the loss iswas probable of occurring. Under this ASU, the income statement will reflect an entity’s current estimate of all expected credit losses. The measurement of expected credit losses will be based upon historical experience, current conditions, and reasonable and supportable forecasts that affect the collectability of the reported amount. Credit losses relating to available-for-sale debt securities will be recorded through an allowance for credit losses rather than as a direct write-down of the security. This ASU is effective for annual periods beginning after December 15, 2019, including interim periods within those annual reporting periods, and early adoption is permitted. The Company adopted the new standard effective January 1, 2020 using the modified retrospective method. The adoption of this standard did not have a material impact on the Company’s consolidated financial statements and related disclosures.

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

3. Collaboration agreements

In June 2014, the Company entered into a Collaboration and Commercial License Agreement with Merck KGaA (the Merck KGaA Agreement). Upon the execution of the agreement, Merck KGaA paid the Company a nonrefundable technology access fee of $12,000 for the right to develop ADCs directed to ~~six~~6 exclusive targets over a specified period of time. NoNaN additional fees are due when a target is designated and the commercial license to the target is granted. Merck KGaA will be responsible for the product development and marketing of any products resulting from this collaboration. All ~~six~~6 targets were designated prior to 2018. The Company is eligible to receive milestones under the Merck KGaA Agreement. The next potential milestone payment is a development milestone of $500 on Merck KGaA’s designation of a preclinical development candidate for ~~any~~a target. Revenue for the milestone is fully constrained until it is certain the milestone would be achieved.

Under the terms of the Merck KGaA Agreement, the Company and Merck KGaA develop research plans to evaluate Merck KGaA's antibodies as ADCs incorporating the Company's technology. The Company receives reimbursement for its efforts under the research plans. The goal of the research plans is to provide Merck KGaA with sufficient information to formally nominate a development candidate and begin IND-enabling studies or cease development on the designated target.

In May 2018, the Company entered into a Supply Agreement with Merck KGaA (the Merck KGaA Supply Agreement). Under the terms of the Merck KGaA Supply Agreement, the Company will provide Merck KGaA preclinical non-GMP ADC Drug Substance and clinical GMP Drug Substance for use in clinical trials associated with one of the antibodies designated under the Merck KGaA Agreement. The Company receives fees for its efforts under the Merck KGaA Supply Agreement and reimbursement equal to the supply cost. The Company may also enter into future supply agreements to provide clinical supply material should Merck KGaA pursue clinical development of any other candidates nominated under the Merck KGaA Agreement.

The Company identified the following performance obligations under the Merck KGaA agreement: (i) exclusive license and research services for six designated targets, (ii) rights to future technological improvements and (iii) participation of project team leaders and providing joint research committee services.

The Company is recognizing revenue related to the exclusive license and research and development services over the estimated period of the research and development services using a proportional performance model. The Company measures proportional performance based on the costs incurred relative to the total costs expected to be incurred. To the extent that the Company receives fees for the research services as they are performed, these amounts are recorded as deferred revenue. Revenue related to future technological improvements and joint research committee services will be recognized ratably over the respective performance period (which in the case of the joint research committee services approximates the time and cost incurred each period), which are 10 and five years, respectively. The Company is continuing to reassess the estimated remaining term at each subsequent reporting period.

As of December 31, 2019, the total transaction price for the Merck KGaA Agreement was $21,500, which represented the amount of consideration the Company was expected to receive for the transfer of goods and services to Merck KGaA. During the nine months ended September 30, 2020, the Company decreased the fees expected to be received for research and development activities by $175 to $6,325, resulting in a revised total transaction price for the Merck KGaA Agreement of $21,325.

During the nine months ended September 30, 2020, the Company completed its performance obligations associated with 1 of the 6 designated targets. For the three months ended ~~March 31,~~September 30, 2020 and 2019, and the nine months ended September 30, 2020 and 2019, the Company recorded collaboration revenue of $11, $800, $817, and ~~$18,~~$836, respectively, related to its efforts under the Merck KGaA Agreement. During the three and nine months ended ~~March 31, 2020~~

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

September 30, 2019, the Company recognized $0$34 and ~~$1,037,~~$1,255, respectively, in collaboration revenue and corresponding research and development expense of $34 and $1,255, respectively, related to the Merck KGaA Supply Agreement.

As of ~~March 31,~~September 30, 2020 and December 31, 2019, the Company had ~~$4,804~~$3,998 and $4,815, respectively, in deferred revenue related to the Merck KGaA Agreement and Merck KGaA Supply Agreement that will be recognized over the remaining performance period.

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~~Mersana Therapeutics, Inc.~~

~~Notes to condensed consolidated financial statements (continued)~~

~~(in thousands, except share and per share data)~~

~~(unaudited)~~

Takeda XMT-1522 Strategic Partnership

In January 2016, the Company entered into a Development Collaboration and Commercial License Agreement with ~~Takeda’s~~Takeda's wholly owned subsidiary, Millennium Pharmaceuticals, Inc. for the development and commercialization of XMT-1522 (the XMT-1522 Agreement). Under the XMT-1522 Agreement, Takeda was granted the exclusive right to commercialize XMT-1522 outside of the United States and Canada. Under the XMT-1522 Agreement, the Company was responsible for conducting certain Phase 1 development activities for XMT-1522, including the ongoing Phase 1 clinical trial, at its own expense. The parties agreed to collaborate on the further development of XMT-1522 in accordance with a global development plan (Post-Phase 1 Development). On January 2, 2019, the Company received notice from Takeda stating that Takeda was exercising its right to terminate the XMT-1522 Agreement upon 30 days’ prior written notice. The XMT-1522 Agreement terminated in accordance with its provisions, and the Company and Takeda wound down activities related to the XMT-1522 Agreement as of March 31, 2019. Under the XMT-1522 Agreement, the Company and Takeda shared equally all budgeted Post-Phase 1 Development costs through the date of termination and for a period of 30 days after the effective termination date.

For the applicable period within the three months ended March 31, 2019, the Company was billed $200 by Takeda, representing the Company’s share of Post-Phase 1 Development costs incurred by Takeda. This amount has been reflected as research and development costs in the consolidated statement of operations.

Takeda strategic research and development partnership

In March 2014, the Company entered into a Research Collaboration and Commercial License Agreement with Takeda through Takeda’s wholly owned subsidiary, Millennium Pharmaceuticals, Inc. (the 2014 Agreement). The 2014 Agreement was amended in January 2015 and amended and restated in January 2016 (the 2016 Restated Agreement). The agreements provided Takeda with the right to develop ADCs directed to a total of ~~seven~~7 exclusive targets, designated by Takeda, over a specified period of time. On January 2, 2019, the Company received notice from Takeda stating that Takeda was exercising its right to terminate the 2016 Restated Agreement upon 45 days’ prior written notice. The 2016 Restated Agreement terminated in accordance with its provisions, and the Company and Takeda wound down activities related to the 2016 Restated Agreement as of March 31, 2019.

During the applicable period within the three months ended March 31, 2019, the Company billed Takeda $195 related to ASC 808 costs.

The Company’s collaboration agreements with Takeda were terminated following receipt of written notices during the first quarter of 2019. As there are no further performance obligations, the Company recognized the remaining deferred revenue of~~$39,965~~ $39,965 related to the termination of the Takeda agreements in the first quarter of 2019.

Included in accounts payable as of ~~March 31,~~September 30, 2020 and December 31, 2019 was $2,335 related to the Takeda agreements.

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

Summary of Contract Assets and Liabilities

The following table presents changes in the balances of our contract assets and liabilities during the ~~three~~nine months ended ~~March 31,~~September 30, 2020 and 2019:


	Balance at Beginning of Period		Additions		Deductions		Balance at End of Period
Nine months ended September 30, 2019
Contract assets	$	0	$	—	$	—	$	0
Contract liabilities:
Deferred revenue	$	46,196	$	0	$	41,550	$	4,646

During the three and nine months ended ~~March 31,~~September 30, 2020 and 2019, the Company recognized the following revenues as a result of changes in the contract asset and the contract liability balances in the respective periods:

The Company has provided limited services for a collaboration partner, Asana BioSciences. For the three and nine months ended ~~March 31, 2020 the Company did not recognize any revenue related to these services and for the three months ended March 31,~~September 30, 2019, the Company recognized ~~$15~~$10 and $25, respectively, of revenue related to these services. The Company did ~~not~~0t recognize any revenue related to ~~milestones in~~these services for the three and nine months ended ~~March 31, 2020 and 2019.~~September 30, 2020. The next potential milestone the Company is eligible to receive is $2,500 upon dosing the fifth patient in a Phase 1 clinical study by Asana BioSciences. As of ~~March 31,~~September 30, 2020, the Company considers this next milestone to be fully constrained as there is considerable judgment involved in determining whether it is probable that a significant revenue reversal would occur. As part of its evaluation of the constraint, the Company considered numerous factors, including the fact that achievement of the milestone is outside the control of the Company and there is a high level of uncertainty in achieving this milestone, as this would require successful initiation of clinical trials by the collaboration partner. The Company reevaluates the probability of achievement of a milestone subject to constraint at each reporting period and as uncertain events are resolved or other changes in circumstances occur.

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

4. Fair value measurements

The following table presents information about the Company's assets and liabilities regularly measured and carried at a fair value and indicates the level within fair value hierarchy of the valuation techniques utilized to determine such value as of ~~March 31, 2020 and~~ December 31, ~~2019:~~

2019. The Company had no marketable securities as of September 30, 2020:

Significant

Quoted Prices

Other

Significant

in Active

Observable

Unobservable

Fair

Markets

Inputs

Inputs


Value

(Level 1)

(Level 2)

(Level 3)
December 31, 2019


Marketable securities:

Commercial paper

$
11,940

$
—

$
11,940

$
—
Corporate bonds

12,010

—

12,010

—
U.S. Treasuries

13,489

13,489

—

—

$
37,439

$
13,489

$
23,950

$
—

The carrying amounts reflected in the consolidated balance sheets for prepaid expenses and other current assets, accounts payable and accrued expenses approximate their fair values due to their short-term nature.

As of ~~March 31,~~September 30, 2020, the carrying value of the Company’s outstanding borrowing under the Amended Credit Facility (as defined below) approximated fair value (a Level 2 fair value measurement), reflecting interest rates currently available to the Company. The Amended Credit Facility is discussed in more detail in Note 8,7, “Debt”.

5. Marketable securities

The following table summarizes marketable securities held at ~~March 31, 2020 and~~ December 31, ~~2019:~~

2019. The Company had 0 marketable securities as of September 30, 2020:

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

Gross

Gross

Amortized

Unrealized

Unrealized

Fair


Cost

Gains

Losses

Value
December 31, 2019

Commercial paper

$
11,940

$
—

$
—

$
11,940
Corporate bonds

11,990

20

—

12,010
U.S. Treasuries

13,484

5

—

13,489

$
37,414

$
25

$
—

$
37,439

As of March 31, 2020, the Company held three securities that were in an unrealized loss position. The aggregate fair value of securities held by the Company in an unrealized loss position at March 31, 2020 was $8,993. These securities were in a gain position as of December 31, 2019. The Company determined that there was no material change in the credit risk of these securities. The Company does not intend to sell these securities and it is not more likely than not that the Company will be required to sell these securities before recovery of their amortized cost bases, which may be at maturity.

The Company has reviewed securities in an unrealized loss position at the individual security level and evaluated current expected credit loss by considering factors such as the nature of the investments, historical experience, market data, issuer-specific factors, and current economic conditions. During the three months ended March 31, 2020, the Company recognized no year-to-date credit loss related to short term marketable securities, and had no allowance for credit loss recorded as of March 31, 2020.

6. Accrued expenses

Accrued expenses consisted of the following as of ~~March 31,~~September 30, 2020 and December 31, 2019:

7. ~~Earnings per share~~

~~The following table presents the calculation of basic and diluted net income per share:~~

Three months ended

March 31,

2020

2019
Numerator:

Net income (loss)

$
(16,926)

$
21,901
Denominator:

Weighted-average number of shares - basic

47,988,630

30,299,650
Dilutive securities - share-based awards

—

1,052,730
Dilutive securities - common stock warrants

—

109,316
Weighted-average number of shares - diluted

47,988,630

31,461,696

Net income (loss) per share - basic

$
(0.35)

$
0.72
Net income (loss) per share - diluted

$
(0.35)

$
0.70

Debt

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~~Mersana Therapeutics, Inc.~~

~~Notes to condensed consolidated financial statements (continued)~~

~~(in thousands, except share and per share data)~~

~~(unaudited)~~

~~Anti-dilutive stock-based awards excluded from the calculation of diluted EPS for the three months ended March 31, 2019 were 2,686,700.~~

For the three months ended March 31, 2020, potentially dilutive securities were excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive, therefore basic and diluted net loss per share were the same for the three months ended March 31, 2020.

~~8. Debt~~

On May 8, 2019, the Company entered into a loan and security agreement (the ~~Credit Facility)~~Original Agreement) with Silicon Valley Bank (SVB) pursuant to which the Company borrowed $5,000. The Original Agreement accrued interest at a floating per annum rate equal to the greater of (i) 4.0% and (ii) 1.50% below the Prime Rate. The Original Agreement had an interest-only period through August 31, 2020.

On August 28, 2020 (the Effective Date), the Company entered into a second amendment (the Amendment) to its existing loan and security agreement (as amended prior to the Amendment, the Existing Credit Facility) with SVB. Pursuant to the Amendment, the Company can borrow term loans in an aggregate amount of $30,000 (the Amended Credit Facility), at its option, (i) up to ~~$20,000,~~$25,000 in up to ~~four~~five principal advances ~~of at least~~through April 30, 2022, and (ii) an additional $5,000 ~~each (each, a Term Loan or collectively,~~in one principal advance, if the ~~Term Loans)~~Company reaches certain development milestone events, as described in the Amendment, through ~~August 31, 2020.~~April 30, 2022. The Company drew ~~$5,000 on the Term Loan~~$5,200 upon execution of the Amendment, the proceeds of which were used to repay the Company’s existing balance and satisfy its obligations to SVB, including the final payment obligation under the Existing Credit Facility.

The Amended Credit Facility bears interest at a floating per annum rate equal to the ~~event~~greater of (i) 4.25% and (ii) 1.00% above the Prime Rate, as defined. The Company is obligated to make monthly interest-only payments on each outstanding term loan commencing on the first calendar day of the month following the funding date of such term loan, and continuing on the first calendar day of each month thereafter through May 31, 2022. The interest only period may be extended through January 31, 2023 upon the achievement of a regulatory milestone, as described in the Amendment. Following the interest-only period, the Company ~~has~~will be required to repay the outstanding principal balance under the term loans in equal monthly payments plus interest in arrears to SVB through November 1, 2024 (the Maturity Date).

The Company is also required to make a final payment to SVB equal to 5.5% of the original principal amount of the term loans then extended to the Company. This final payment is accreted under the effective interest method over the life of each term loan. The term loans are secured by substantially all of the Company's assets, except for its intellectual property which is subject to a negative pledge, and certain other customary exclusions.

At the Company’s option, it may prepay the outstanding principal balance of any term loans in whole but not ~~borrowed~~in part, subject to a ~~total~~prepayment fee of: (a) 3.0% of ~~$20,000 upon~~ the ~~earlier of~~term loans then extended to the Company if the prepayment occurs on or prior to August ~~21, 2020, acceleration~~28, 2021, (b) 2.0% of the term loans then extended to the Company if the prepayment occurs after August 28, 2021 but on or prior to August 28, 2022, or (c) 1.0% of the term loans then extended to the Company if the prepayment occurs after August 28, 2022 but before November 1, 2024. The Amended Credit Facility includes customary affirmative and restrictive covenants applicable to the Company. Affirmative covenants include, among others, covenants requiring the Company to maintain its corporate existence and governmental approvals, deliver certain financial reports, maintain insurance coverage and satisfy certain requirements regarding

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

deposit accounts. The Amendment removed the requirement for the Company to maintain a minimum liquidity ratio. The restrictive covenants include, among others, requirements relating to the Company’s ability to transfer collateral, incur additional indebtedness, engage in mergers or acquisitions, pay dividends or make other distributions, make investments, create liens, sell assets and agree to a change in control, in each case subject to certain customary exceptions.

The Company’s payment obligations under the Amended Credit Facility are subject to acceleration upon the occurrence of specified events of default, which include, but are not limited to, the occurrence of a material adverse change in the Company’s business, operations, or ~~Company’s prepayment~~financial or other condition. Amounts outstanding upon the occurrence of an event of default are payable upon SVB’s demand and shall accrue interest at an additional rate of 5.0% per annum of the ~~then extended Term Loans, the Company is required to pay an additional fee equal to 3.0% of any unborrowed portion of the committed funding (the Unused Term Loan Commitment Fee).~~

past due amount outstanding. As of ~~March 31,~~September 30, 2020, the Company was in compliance with all covenants under the Amended Credit Facility. As such, as of ~~March 31,~~September 30, 2020, the classification of the loan balance as stated on the balance sheet was based on the timing of defined future payment obligations.

The unamortized issuance costs under the Existing Credit Facility were $139 as of the date of the Amendment. The Company incurred debt issuance costs paid to the lender in connection with the Amended Credit Facility of $17. The Company recorded such costs, including the settlement of the final payment obligation under the Existing Credit Facility as a discount from the carrying value of the term loans which are amortized as interest expense using the effective-interest method over the term of the Amended Credit Facility.

As of ~~March 31,~~September 30, 2020, there was $5,200 in term loans outstanding under the ~~Company had drawn a Term Loan of $5,000.~~

~~As of March 31, 2020,~~Amended Credit Facility and the debt consisted of the following:

March 31,

2020
Total debt

$
5,000
Less: Current portion of long-term-debt

(1,167)
Total debt, net of current portion

3,833
Debt financing costs, net of accretion

(163)
Accretion related to final payment

62
Long-term debt, net

$
3,732


	September 30, 2020
Total debt	$	5,200


Debt financing costs, net of accretion	(262)
Accretion related to final payment	6
Long-term debt, net	$	4,944

As of ~~March 31,~~September 30, 2020, the estimated future principal payments due are as follows:

During the three months ended ~~March 31,~~September 30, 2020 and 2019, and the nine months ended September 30, 2020 and 2019, the Company recognized $60, $51, $173 and $64, respectively, of interest expense related to the Existing Credit ~~Facility.~~

Facility and Amended Credit Facility, as applicable.

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~~Mersana Therapeutics, Inc.~~

~~Notes to condensed consolidated financial statements (continued)~~

~~(in thousands, except share and per share data)~~

~~(unaudited)~~

9.8. Stockholders’ equity

As of ~~March 31,~~September 30, 2020, the Company had 25,000,000 shares of authorized preferred stock. NoNaN shares of preferred stock have been issued.

~~Common stock~~

~~The holders~~

Table of ~~the common stock are entitled~~Contents

Mersana Therapeutics, Inc.

Notes to ~~one vote for each~~condensed consolidated financial statements (continued)

(in thousands, except share ~~held. Common stockholders are not entitled to receive dividends, unless declared by the Board of Directors (the Board).~~

~~At March 31, 2020~~ and ~~December 31, 2019, there were 6,848,955 and 7,782,582, respectively, shares of common stock reserved for the exercise of outstanding stock options, restricted stock units and warrants.~~

per share data)

March 31,

December 31,

2020

2019
Stock options

6,049,288

4,720,772
Restricted stock units

760,193

447,336
Warrants

39,474

39,474
Exchange warrants

—

2,575,000

6,848,955

7,782,582
(unaudited)

At-the-market equity offering program

In July 2, 2018, the Company established an at-the-market (ATM) equity offering program ~~(ATM)~~(the 2018 ATM) pursuant to which it ~~is able to offer~~offered and ~~sell~~sold up to $75,000 of its common stock from time to time at prevailing market prices. In April 2020, the Company sold 8,938,599 and 1,962,000 shares of common stock at $5.59 per share and $7.74 per share, respectively, to raise aggregate gross proceeds of $65,153 through the 2018 ATM facility. Net proceeds to the Company after deducting fees, commissions and other expenses related to the offering were approximately $62,976.

In May 2020, the Company terminated the 2018 ATM and established a new ATM equity offering program (the 2020 ATM) pursuant to which it is able to sell up to $100,000 of its common stock from time to time at prevailing market prices. As of ~~March 31,~~September 30, 2020, the Company had ~~not~~0t sold any shares under the 2020 ATM.

In June 2020, the Company sold 9,200,000 shares of common stock, in an underwritten public offering price to the public of $19.00 per share, resulting in gross proceeds of approximately $174,800. Net proceeds to the Company after deducting fees, commissions and other expenses related to the offering were approximately $163,991.

In connection with a 2013 Series A-1 Preferred Stock issuance, the Company granted to certain investors warrants to purchase 129,491 shares of common stock. The warrants have a $0.05 per share exercise price and a contractual life of 10 years. The fair value of these warrants was recorded as a component of equity at the time of issuance. As of ~~March 31,~~September 30, 2020,, there were warrants to purchase 39,474 shares of common stock.

Exchange ~~Warrants~~

warrants

On November 26, 2019, the Company entered into an exchange agreement with entities affiliated with Biotechnology Value Fund, L.P. (the ~~“Exchanging Stockholders”)~~Exchanging Stockholders), pursuant to which the Exchanging Stockholders exchanged an aggregate of 2,575,000 shares of common stock for warrants (the ~~“Exchange Warrants”)~~Exchange Warrants) to purchase an aggregate of 2,575,000 shares of common stock (subject to adjustment in the event of any stock dividends and splits, reverse stock split, merger or consolidation, change of control, reorganization or similar transaction, as described in the Exchange Warrants), with an exercise price of $0.0001 per share.

On March 2, 2020, the Exchanging Stockholders exercised the Exchange Warrants in full on a net cashless exercise basis, resulting in the issuance of 2,574,971 shares of common stock.

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

~~10.~~At September 30, 2020 and December 31, 2019, there were 6,995,704 and 7,782,582, respectively, shares of common stock reserved for the exercise of outstanding stock options, restricted stock units and warrants, as follows:


	September 30, 2020	December 31, 2019
Stock options	6,215,368	4,720,772
Restricted stock units	740,862	447,336
Warrants	39,474	39,474
Exchange warrants	0	2,575,000
	6,995,704	7,782,582

In June 2017, the Company’s ~~shareholders~~stockholders approved the 2017 Stock Incentive Plan (the 2017 Plan). Under the 2017 Plan, up to 2,255,000 shares of common stock were initially available to be granted to the Company's employees, officers, directors, consultants and advisors in the form of options, restricted stock units (RSUs) or other stock-based awards. The number of shares of common stock issuable under the 2017 Plan will be cumulatively increased annually by 4% of the outstanding shares or such lesser amount specified by the Board. The terms of the awards are determined by the Board, subject to the provisions of the 2017 Plan. Any cancellations under the 2007 Plan, which expired in June 2017, would increase the number of shares that could be granted under the 2017 Plan. In January 2020, the number of shares of common stock issuable under the 2017 Plan was increased by 1,815,520 shares. As of ~~March 31,~~September 30, 2020, there were ~~1,642,679~~1,320,916 shares available for future issuance under the 2017 Plan.

During the nine months ended September 30, 2020, the Company granted 2,165,306 RSUs and options to purchase shares of common stock to employees under the 2017 Plan.

On September 2, 2020, the Company granted its senior vice president of regulatory affairs an option to purchase up to 120,000 shares of common stock as an inducement to employment in accordance with Nasdaq Listing Rule 5635(c)(4). No underwriters were involved in this issuance of securities. The securities were issued pursuant to Section 4(a)(2) under the Securities Act of 1933, as amended, relating to transactions by an issuer not involving any public offering. These options are subject to terms substantially the same as the 2017 Plan.

With respect to ~~incentive~~the stock ~~options,~~option grants as described above, the exercise price per share will equal the fair market value of the common stock on the date of grant, and the vesting period is generally four years. Nonqualified stock options will be granted at an exercise price established by the Board at its sole discretion (which has not been less than fair market value on the date of grant) and the vesting periods may vary. Options granted ~~under the 2017 Plan~~as described above expire no later than 10 years from the date of grant. The Board may accelerate vesting or extend the expiration of granted options in the case of a merger, consolidation, dissolution, or liquidation of the Company.

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

Stock option activity

A summary of the options activity under the Plans is as follows:

The weighted-average grant date fair value of options granted during the ~~three~~nine months ended ~~March 31,~~September 30, 2020 and 2019, was $~~3.79~~$6.17 and $~~2.39~~$2.47 per share, respectively.

Cash received from the exercise of stock options was ~~$119~~$1,732 and $42$121 for the ~~three~~nine months ended ~~March 31,~~September 30, 2020 and 2019, respectively.

Restricted stock units

(RSUs)

In July 2019, the Company issued RSUs with service conditions to employees. The awards cliff-vest two years after the grant date. In January 2020, the Company issued 324,932 RSUs with a service condition to employees for which the

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~~Mersana Therapeutics, Inc.~~

~~Notes to condensed consolidated financial statements (continued)~~

~~(in thousands, except share and per share data)~~

~~(unaudited)~~

vesting term is annually over four years. Vesting of these awards is contingent on the fulfillment of the service conditions during the vesting term.

A summary of the RSU activity under the 2017 Plan is as follows:


					Number of Shares
			~~of Shares~~

Unvested at January 1, 2020	447,336	~~447,336~~
Granted		324,932		~~324,932~~
Vested		0		—
Forfeited		(31,406)		~~(12,075)~~
Unvested at ~~March 31,~~September 30, 2020		740,862		~~760,193~~

Stock-based compensation expense

The Company uses the provisions of ASC 718, Stock Compensation, to account for all stock-based awards to employees and ~~nonemployees.~~

non-employees.

The measurement date for employee awards is generally the date of grant. Stock-based compensation expense is recognized over the requisite service period, which is generally the vesting period, using the straight-line method.

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

The following table presents stock-based compensation expense by award type included within the Company’s condensed consolidated statement of operations and comprehensive loss:

The following table presents stock-based compensation expense as reflected in the Company’s condensed consolidated statements of operations and comprehensive loss:

Three months ended

March 31,

2020

2019
Research and development

$
797

$
516
General and administrative

812

648
Stock-based compensation expense included in Total operating expenses

$
1,609

$
1,164


	Three Months Ended September 30,				Nine Months Ended September 30,
	2020		2019		2020		2019
Research and development	$	952	$	587	$	2,554	$	1,636
General and administrative	966		698		2,629		1,974
Stock-based compensation expense included in Total operating expenses	$	1,918	$	1,285	$	5,183	$	3,610

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~~Mersana Therapeutics, Inc.~~

~~Notes to condensed consolidated financial statements (continued)~~

~~(in thousands, except share and per share data)~~

~~(unaudited)~~

As of ~~March 31,~~September 30, 2020, there was ~~$11,341~~$15,007 and ~~$3,022~~ $2,269 of unrecognized stock compensation expense related to unvested stock options and unvested RSUs, respectively, that is expected to be recognized over a weighted-average period of 2.5 years and ~~2.9 years.~~

2.6 years, respectively.

The fair value of each option award is estimated on the date of grant using the Black-Scholes option pricing model with the following weighted average assumptions:

Employee Stock Purchase Plan

During the year ended December 31, 2017, the Board adopted, and the Company’s stockholders approved the 2017 employee stock purchase plan (the 2017 ESPP). The Company initially reserved 225,000 shares of common stock for issuance under the 2017 ESPP. In January 2020, the number of shares of common stock for issuance under the 2017 ESPP was increased by 450,000 shares. For the nine months ended September 30, 2020 and 2019, the Company issued 68,419 and 82,281, respectively, shares under the 2017 ESPP. The Company did ~~not~~0t issue any shares under the 2017 ESPP ~~during~~for the three months ended ~~March 31,~~September 30, 2020 and 2019. As of ~~March 31,~~September 30, 2020, there were ~~725,085~~656,666 shares available for issuance under the 2017 ESPP.

~~11.~~

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Mersana Therapeutics, Inc.

Notes to condensed consolidated financial statements (continued)

(in thousands, except share and per share data)

(unaudited)

The Company has an operating lease for its office space in Cambridge, MA and operating and finance leases for certain equipment. In March 2020, the Company entered into the Seventh Amendment to the office space lease to extend the term of the lease through March 2026 and to provide the Company with a tenant improvement allowance of $172. The current rate per square foot that is in place through March 2021 (the original expiration date of the lease) did not change. After March 2021, there are predetermined fixed escalations of the rate as outlined in the amendment. The Company has an option to extend the lease term for an additional five years. The Company’s exercise of this option was not considered reasonably certain as of ~~March 31,~~September 30, 2020.

The extension is accounted for as a lease modification. The Company assessed the lease classification of the amended office space lease at the modification date and determined that the amended office space lease should be accounted for as an operating lease. The right-of-use asset and corresponding operating lease liability have been remeasured based on the present value of remaining lease payments over the remaining extended lease term, using the incremental borrowing rate applicable as of the lease modification date. The Company determined the appropriate incremental borrowing rate by using a synthetic credit rating which was estimated based on an analysis of outstanding debt of companies with similar credit and financial profiles. Since the operating lease is a net lease, as the non-lease components (i.e., common area maintenance) are paid separately from rent based on actual costs incurred, such non-lease components were not included in the right-of-use asset and liability and are reflected as an expense in the period incurred.

As a result of the modification in March 2020, the Company recorded an increase of $9,980 to its right-of-use (ROU) asset and lease ~~liabilities.~~

liabilities in the first quarter of 2020.

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~~Mersana Therapeutics, Inc.~~

~~Notes to condensed consolidated financial statements (continued)~~

~~(in thousands, except share and per share data)~~

~~(unaudited)~~

Following the change, the ~~Company’s~~Company's future minimum lease payments under non-cancellable leases as of ~~March 31,~~September 30, 2020 were as follows:

Through ~~March 31,~~September 30, 2020, the Company had licensed intellectual property from ~~two~~3 biotechnology companies. The consideration included upfront payments and a commitment to pay annual license fees, milestone payments and, upon product commercialization, royalties on revenue generated from the sale of products covered by the licenses. The Company recorded a $750 milestone payment for the dosing of the first patient in the XMT-1592 trial during the nine months ended September 30, 2020. The Company recorded a milestone payment of $600 during the three and nine months ended September 30, 2019 upon the dosing of the first patient in the expansion cohort of the XMT-1536 clinical trial. The Company did ~~not~~0t record any milestone payments during the three months ended ~~March 31, 2020 and 2019.~~

~~13. Subsequent Events~~

On July 2, 2018, the Company established an at-the-market equity offering program (ATM) pursuant to which it is able to offer and sell up to $75,000 of its common stock from time to time at prevailing market prices. As of March 31, 2020, the Company had not sold any shares under the ATM. On April 7, 2020, the Company sold 8,938,599 and 1,962,000 shares of common stock at~~$5.59 per share and $7.74 per share, respectively, to raise gross proceeds of $65,153 through this ATM facility.~~

September 30, 2020.

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

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our unaudited condensed consolidated financial statements and the accompanying notes appearing elsewhere in this Quarterly Report on Form 10-Q and the audited financial statements and the accompanying notes included in our Annual Report on Form 10-K for the year ended December 31, 2019 filed with the Securities and Exchange Commission (SEC) on February 28, 2020.

Our actual results and the timing of certain events may differ materially from the results discussed, projected, anticipated, or indicated in any forward-looking statements. We caution you that forward-looking statements are not guarantees of future performance and that our actual results of operations, financial condition and liquidity, and the development of the industry in which we operate may differ materially from the forward-looking statements contained in this Quarterly Report. In addition, even if our results of operations, financial condition and liquidity, and the development of the industry in which we operate are consistent with the forward-looking statements contained in this Quarterly Report, they may not be predictive of results or developments in future periods.

The following information and any forward-looking statements should be considered in light of factors discussed elsewhere in this Quarterly Report on Form 10-Q, ~~including those risks identified under Part II, Item 1A. Risk Factors, and~~ in our Annual Report on Form 10-K for the year ended December 31, 2019, filed with the SEC on February 28, 2020, and in our Quarterly Report on Form 10-Q for the quarterly period ending March 31, 2020, filed with the SEC on May 8, 2020, including those risks identified under Item 1A. Risk Factors.

We caution readers not to place undue reliance on any forward-looking statements made by us, which speak only as of the date they are made. We disclaim any obligation, except as specifically required by law and the rules of the SEC, to publicly update or revise any such statements to reflect any change in our expectations or in events, conditions or circumstances on which any such statements may be based, or that may affect the likelihood that actual results will differ from those set forth in the forward-looking statements.

Overview

We are a clinical-stage biopharmaceutical company focused on developing antibody drug conjugates, or ADCs, that offer a clinically meaningful benefit for cancer patients with significant unmet need. We have leveraged 20 years of industry learning in the ADC field to develop proprietary and differentiated technology platforms that enable us to design ADCs to have improved efficacy, safety and tolerability relative to existing ADC therapies.

We believe that our innovative platforms which include Dolaflexin and Dolasynthen, each delivering our DolaLock payload, as well as Immunosynthen, delivering a novel stimulator of interferon genes, or STING, agonist, provide a ~~highly efficient~~highly-efficient product engine that has enabled a robust discovery pipeline for us and our partners. Our ADCs in preclinical and clinical studies are first-in-class molecules that target multiple tumor types with high unmet medical need and have exhibited improved safety and efficacy compared to ADCs developed using first-generation technology.

Our goal is to become a leading oncology company by leveraging the potential of our innovative and differentiated ADC technologies and the experience and competencies of our management team to identify, acquire and develop promising ADC product candidates and to commercialize cancer therapeutics that are improvements over existing treatments.

XMT-1536, a first-in-class ADC targeting the sodium-dependent phosphate transport protein NaPi2b, utilizes the Dolaflexin platform to deliver an average of 10 to 12 auristatin DolaLock payload molecules per antibody. The NaPi2b antigen is broadly expressed in non-small cell lung cancer, or NSCLC, adenocarcinoma and ovarian cancer with limited expression in normal tissue. We are actively recruiting and dosing patients with ovarian cancer and NSCLC adenocarcinoma, where a majority of patients express NaPi2b, in a Phase 1 clinical trial.

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We have also selected our next clinical product candidate, XMT-1592. XMT-1592 uses one of our new platforms, Dolasynthen, and also targets NaPi2b. XMT-1592 comprises the same proprietary NaPi2b antibody and potent auristatin DolaLock payload with controlled bystander effect as XMT-1536, with the additional features of homogeneous, site-specific bioconjugation and precise drug-to-antibody ratio, or DAR. We filed an Investigational New Drug (IND) application in the first quarter of 2020 ~~which was approved by the U.S. Food~~ and ~~Drug Administration (FDA). We remain on track to initiate~~initiated the Phase 1 dose escalation study of XMT-1592 in the second quarter of 2020.

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Our ~~early stage~~early-stage programs include a potentially first-in-class B7-H4-targeted DolaLock ~~ADC addressing areas of high unmet medical need.~~ADC. Our objective is to rapidly progress through IND-enabling studies and scale up manufacturing activities with third parties. B7-H4 provides significant opportunities for development in areas of high unmet need such as breast cancer, NSCLC and ovarian cancer.

In addition, we have established strategic research and development partnerships with Merck KGaA and Asana Biosciences for the development and commercialization of additional ADC product candidates against a limited number of targets selected by our partners based on our Fleximer platform. We believe the potential of our ADC technologies, supported by our ~~world class~~world-class management team and protected by our robust intellectual property portfolio, will allow us to develop targeted and highly tailored therapies to help cancer patients become cancer survivors.

Since inception, our operations have focused on such matters as building our platforms, identifying potential product candidates, producing drug substance and drug product material for use in preclinical studies, conducting preclinical and toxicology studies, manufacturing clinical study material and conducting clinical studies, establishing and protecting our intellectual property, staffing our company and raising capital. We do not have any products approved for sale and have not generated any revenue from product sales. We have funded our operations primarily through our strategic partnerships, private placements of our convertible preferred stock and public offerings of our common stock. OnIn April 7, 2020, we sold ~~8.9 million and 2.0~~approximately 10.9 million shares of common stock ~~at $5.59 per share~~ and ~~$7.74 per share, respectively, to raise gross~~received net proceeds of ~~approximately $65~~$63.0 million. In addition, in June 2020, we sold 9.2 million ~~through our at-the-market equity offering program, or ATM.~~

shares of common stock and received net proceeds of $164.0 million.

Since inception, we have incurred significant cumulative operating losses. For the ~~three~~nine months ended ~~March 31,~~September 30, 2020, the net loss was ~~$16.9~~$59.2 million, compared to net ~~income~~loss of ~~$21.9~~$12.0 million in the ~~three~~nine months ended ~~March 31,~~September 30, 2019. The difference year over year is primarily attributable to $40.0 million in revenue that was recognized in the first quarter of 2019 as a result of the discontinuation of the partnership with Takeda in that ~~quarter~~. quarter. As of ~~March 31,~~September 30, 2020, we had an accumulated deficit of ~~$209.3~~$251.6 million. We expect to continue to incur significant expenses and operating losses over the next several years. We anticipate that our expenses will increase significantly in connection with our ongoing activities, as we:

~~continue clinical development activities for our lead product candidate XMT-1536 and initiate clinical development activities for XMT-1592;~~

~~develop a research assay and companion diagnostic for the NaPi2b biomarker;~~

•continue clinical development activities for our lead product candidates XMT-1536 and XMT-1592;

~~continue activities to discover, validate and develop additional product candidates;~~

•develop a research assay and companion diagnostic for the NaPi2b biomarker;

~~maintain, expand and protect our intellectual property portfolio; and~~

•continue activities to discover, validate and develop additional product candidates;

~~hire additional research, development and general and administrative personnel.~~

•maintain, expand and protect our intellectual property portfolio; and

•hire additional research, development and general and administrative personnel.

Impact of COVID-19 on Our Business

~~The coronavirus pandemic continues to evolve rapidly.~~

We are ~~monitoring~~continuing to monitor the impact of the COVID-19 pandemic on our operations and ongoing clinical and preclinical development, as well as discovery efforts. Mitigation activities to minimize COVID-19-related operation disruptions are ongoing and include:

In line with guidance from the U.S. Centers for Disease Control and Prevention (CDC) and the state of Massachusetts, we have implemented work from home measures for all non-laboratory employees and have suspended all business travel. We have also prioritized laboratory activities and implemented staggered schedules in the interest of safety and efficiency for any laboratory-based employees.

We are currently working with over 20 investigational sites in different geographic areas across the United States which are enrolling patients in the XMT-1536 Phase 1 study. Consistent with FDA guidance, we issued an administrative letter to allow for remote patient monitoring and remote testing, when possible. Most of the study sites continue to enroll patients in the study. At this time and subject to further COVID-19 implications to patient enrollment, we expect to be able to present more mature data from the expansion portion of the study in the second half of 2020.

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•In line with guidance from the U.S. Centers for Disease Control and Prevention (CDC) and the Commonwealth of Massachusetts, we have implemented work from home measures for all non-laboratory employees and have suspended all business travel. We have also prioritized laboratory activities and implemented staggered schedules in the interest of safety and efficiency for laboratory-based employees. We will continue to modify and adapt our measures to align with guidance as the pandemic evolves.

We believe we have sufficient inventory of XMT-1536 and XMT-1592 to support our ongoing and planned clinical studies as well as sufficient inventory of advanced intermediates stockpiled in the United States to support more than two years of manufacturing of drug substance and product. At this time and subject to further COVID-19 implications, we do not anticipate any disruptions to its clinical supply.

•We are currently enrolling patients at investigational sites in different geographic areas across the United States, Canada and Australia in the XMT-1536 Phase 1 study and within the United States in the XMT-1592 Phase 1 dose escalation study. We are in the process of initiating additional clinical sites both inside and outside the United States to increase enrollment, which could additionally mitigate potential regional impacts from COVID-19. Consistent with FDA guidance, we issued an administrative letter to allow for remote patient monitoring and remote testing, when possible.

•To the best of our knowledge, our contract manufacturing partners continue to operate their manufacturing facilities at or near normal levels, and we have not experienced any COVID-related delays in our manufacturing to date. We believe we have sufficient inventory of XMT-1536 and XMT-1592 to support our ongoing clinical studies. We have planned manufacturing runs to address all currently anticipated future needs. At this time, and subject to further COVID-19 implications, we do not anticipate any disruptions to our clinical supply.

The ultimate impact of the coronavirus pandemic on our business operations is highly uncertain and subject to change and will depend on future developments, which cannot be accurately predicted. While the pandemic did not materially affect our financial results and business operations in the ~~first~~third quarter ended ~~March 31,~~September 30, 2020, we are unable to predict the impact that COVID-19 will have on our financial position and operating results in future periods due to numerous uncertainties. Management is actively monitoring this situation and the possible effects on our financial condition, operations, suppliers, industry, and our employees. For additional information about risks and uncertainties related to the COVID-19 pandemic that may impact our business, our financial condition or our results of operations, see “Part II, Item 1A—Risk Factors” below in ~~this~~the Company’s Quarterly Report on Form ~~10-Q.~~

10-Q for the quarter ended March 31, 2020, filed on May 8, 2020.

Financial operations overview

Revenue

To date, we have not generated any revenue from the sale of products. All of our revenue has been generated from strategic partnerships.

In June 2014, we entered into an agreement with Merck KGaA for the development and commercialization of ADC product candidates utilizing Fleximer for up to six target antigens. Merck KGaA is responsible for generating antibodies against the target antigens and we are responsible for generating Fleximer and our proprietary payloads and conjugating this to the antibody to create the ADC product candidates. Merck KGaA has the exclusive right to and is responsible for the further development and commercialization of these ADC product candidates. In May 2018, we entered into a supply agreement with Merck KGaA for the supply of materials that could be used for IND-enabling studies and clinical trials.

For the three months ended ~~March 31,~~September 30, 2020 ~~and 2019,~~we recognized an immaterial amount of revenue related to the Merck KGaA Agreements. For the nine months ended September 30, 2020 we recognized revenue of ~~an immaterial amount~~$0.8 million and ~~$1.0~~for the three and nine months ended September 30, 2019, we recognized $0.8 million and $2.1 million, respectively, of revenue related to the Merck KGaA agreements.

In January 2016, we entered into collaboration agreements with Takeda for the development and commercialization of XMT-1522, a HER2-targeted ADC, and up to seven ADC product candidates utilizing Fleximer. ~~The Company’s~~Our collaboration agreements with Takeda were terminated during the first quarter of 2019. We recognized the

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remaining deferred revenue of $40.0 million related to the termination of the Takeda agreements in the first quarter of 2019. We do not expect to have any further revenue related to these agreements.

We have provided limited services to Asana BioSciences. For ~~each of~~ the three and nine months ended ~~March 31, 2020 and~~September 30, 2019 we recorded an immaterial amount of revenue related to these services. ~~The Company~~We did not ~~recognize~~record any revenue related to ~~milestones~~these services in the three and nine months ended ~~March 31, 2020 or 2019.~~

September 30, 2020.

For the foreseeable future, we expect substantially all of our revenue to be generated from our collaboration agreements with Merck KGaA and Asana BioSciences. Given the uncertain nature and timing of clinical development, we cannot predict when or whether we will receive further milestone payments or any royalty payments under these collaborations.

Operating expenses

Research and development expenses

Research and development expenses consist primarily of costs incurred for our research and development activities, including our drug discovery efforts, and the development of our product candidates, which include:

~~employee-related expenses, including salaries, bonuses, benefits and stock-based compensation expense;~~

~~costs of funding research and development performed by third parties that conduct research, preclinical activities, manufacturing and clinical trials on our behalf;~~

•employee-related expenses, including salaries, bonuses, benefits and stock-based compensation expense;

•costs of funding research and development performed by third parties that conduct research, preclinical activities, manufacturing and clinical trials on our behalf;

•laboratory supplies;

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•facility costs, including rent, depreciation and maintenance expenses; and

~~laboratory supplies;~~

•upfront and milestone payments under our third-party licensing agreements.

~~facility costs, including rent, depreciation and maintenance expenses; and~~

~~upfront and milestone payments under our third-party licensing agreements.~~

Research and development costs are expensed as incurred. Costs of certain activities, such as manufacturing and preclinical and clinical studies, are generally recognized based on an evaluation of the progress to completion of specific tasks. Costs for certain development activities, such as clinical studies, are recognized based on an evaluation of the progress to completion of specific tasks using data such as patient enrollment, clinical site activations and information provided to us by the third parties with whom we contract.

Research and development activities are central to our business model. Product candidates in later stages of clinical development generally have higher development costs than those in earlier stages of clinical development, primarily due to the increased size and duration of later-stage clinical trials and manufacturing costs. We expect that our total future research and development costs will continue to increase over current levels, depending on the progress of our clinical development programs. There are numerous factors associated with the successful development and commercialization of any of our product candidates, including future trial design and various regulatory requirements, many of which cannot be determined with accuracy at our current stage of development. Additionally, future commercial and regulatory factors beyond our control may impact our clinical development programs and plans.

A significant portion of our research and development costs have been external costs, which we track on a program-by-program basis following nomination as a product candidate. We have not historically tracked all of our internal research and development expenses on a program-by-program basis as they are deployed across multiple projects under development. The following table summarizes our external research and development expenses, by program, following nomination as a development candidate for the three and nine months ended ~~March 31,~~September 30, 2020 and ~~2019.~~2019. All external research and development expenses not attributable to the XMT-1536, XMT-1592 and XMT-1522 programs are captured within preclinical and discovery costs. These costs relate to XMT-1592 prior to its designation in early 2020 as our next ADC clinical candidate, as well as additional earlier discovery stage

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programs and certain unallocated costs. We terminated the development of XMT-1522 in the first quarter of 2019. Our internal research and development costs are primarily personnel-related costs, stock-based compensation costs, and facility costs, including depreciation, and lab consumables. ~~Pre-development candidate expenses, unallocated costs and internal research and development costs have been stated separately.~~


	Three months ended
	March 31,					Three Months Ended September 30,				Nine Months Ended September 30,
(in thousands)	2020		2019		(in thousands)	2020		2019		2020		2019
XMT-1536 external costs	$	2,370	$	2,818	XMT-1536 external costs	$	4,451	$	2,193	$	10,356	$	6,801
XMT-1592 external costs		1,174		—	XMT-1592 external costs	1,149		—		4,994		—
XMT-1522 external costs		—		978	XMT-1522 external costs	—		305		—		2,267
Preclinical and discovery costs		1,507		4,108	Preclinical and discovery costs	3,348		4,994		6,878		13,383
Internal research and development costs		7,168		7,239	Internal research and development costs	7,598		6,209		21,951		20,159
Total research and development costs	$	12,219	$	15,143	Total research and development costs	$	16,546	$	13,701	$	44,179	$	42,610

The successful development of our product candidates is highly uncertain. As such, we cannot reasonably estimate or know the nature, timing and estimated costs of the efforts that will be necessary to complete the remainder of the development of our product candidates. We are also unable to predict when, if ever, material net cash inflows will commence from the development efforts associated with our product candidates. This is due to the numerous risks and uncertainties associated with developing drugs, including the uncertainty of:

~~successful completion of preclinical studies and IND-enabling studies;~~

~~successful enrollment in and completion of clinical trials;~~

•successful completion of preclinical studies and IND-enabling studies;

~~receipt of marketing approvals from applicable regulatory authorities;~~

•successful enrollment in and completion of clinical trials;

~~establishing commercial manufacturing capabilities or making arrangements with third-party manufacturers;~~

•receipt of marketing approvals from applicable regulatory authorities;

•establishing commercial manufacturing capabilities or making arrangements with third-party manufacturers;

•obtaining and maintaining patent and trade secret protection and regulatory exclusivity for our product candidates;

•commercializing the product candidates, if and when approved, whether alone or in collaboration with others; and

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the drugs following approval.

~~obtaining and maintaining patent and trade secret protection and regulatory exclusivity for our product candidates;~~

~~commercializing the product candidates, if and when approved, whether alone or in collaboration with others; and~~

~~continued acceptable safety profile of the drugs following approval.~~

A change in the outcome of any of these or other variables with respect to the development, manufacture or commercialization of any of our product candidates would significantly change the costs, timing and viability associated with the development of that product candidate.

General and administrative expenses

General and administrative expenses consist primarily of salaries and other employee-related costs, including stock-based compensation, for personnel in executive, finance, accounting, business development, legal operations, information technology and human resources functions. Other significant costs include facility costs not otherwise included in research and development expenses, legal and other fees relating to patent and corporate matters, and fees for accounting and consulting services.

We anticipate that our general and administrative expenses will increase in the future to support continued research and development activities, including increased costs related to the hiring of additional personnel, fees to outside consultants and patent costs, among other expenses.

Other income (expense)

Other income (expense) consists primarily of interest income earned on cash equivalents and marketable securities. Interest expense is related to borrowings under the credit facility that we entered into onin May 9, 2019 ~~with Silicon Valley Bank.~~and amended in August 2020. These borrowings bear a floating per annum rate interest, as well as a final payment of 5%5.5% of the amounts drawn, that is being recorded as interest expense over the term through the maturity date using the effective-interest method. Also included in interest expense is the amortization of the deferred financing costs and the accretion of debt discount relating to the credit facility.

Results of Operations

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

The following table summarizes our results of operations for the three months ended ~~March 31,~~September 30, 2020 and 2019:

Collaboration Revenue

Collaboration revenue was immaterial during the three months ended ~~March 31,~~September 30, 2020 and ~~$41.0~~$0.8 million during the three months ended ~~March 31,~~September 30, 2019. The decrease in collaboration revenue was primarily a result of the ~~termination~~completion of ~~the Takeda agreements and the recognition of the remaining deferred revenue of $40.0 million~~research services associated with a target included in the ~~first quarter of 2019. Additionally,~~Merck KGaA Agreement during the three months ended ~~March 31, 2019, collaboration revenue of $1.0 million was recognized related to the Merck KGaA Agreement and Merck KGaA Supply Agreement.~~

September 30, 2019.

Research and Development Expense

Research and development expense ~~decreased~~increased by ~~$2.9~~$2.8 million from ~~$15.1~~$13.7 million for the three months ended ~~March 31,~~September 30, 2019 to ~~$12.2~~$16.5 million for the three months ended ~~March 31,~~September 30, 2020.

The ~~decrease~~increase in research and development expense was primarily attributable to the following:

~~a decrease of $1.4 million related to manufacturing activities for XMT-1536;~~

~~a decrease of $1.2 million because of an upfront payment in 2019 for a technology license fee and timing of research efforts;~~

•an increase of $2.7 million related to manufacturing, clinical and regulatory activities for XMT-1536;

~~a decrease of $0.8 million related to the development and manufacturing activities for XMT-1522; and~~

•an increase of $1.1 million related to employee compensation, primarily due to increased headcount supporting the growth of our research and development activities, and the increase in valuation of stock-based awards granted to employees, resulting in higher stock-based compensation expense;

~~a decrease of $0.7 million to support partner programs.~~

•an increase of $0.5 million related to manufacturing activities for our discovery stage programs;

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•an increase of $0.4 million related to XMT-1592 clinical expenses;

•an increase of $0.4 million related to consulting and professional fees; and

•an increase of $0.2 million related to advancement of companion diagnostic development efforts for the NaPi2B biomarker.

These ~~decreased~~increased costs were partially offset by the following:

~~an increase of approximately $0.9 million related to XMT-1536 clinical and regulatory expenses; and~~

~~an increase of $0.3 million related to advancement of companion diagnostic development efforts for the NaPi2b biomarker.~~

•a decrease of $2.3 million related to preclinical development and manufacturing activities for XMT-1592; and

•a decrease of $0.2 million related to the development and manufacturing activities for XMT-1522.

We expect our research and development expenses to increase as we continue our clinical development of XMT-1536 and XMT-1592 and continue to advance our preclinical product candidate pipeline and invest in improvements in our ADC technologies.

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General and Administrative Expense

General and administrative expense increased by ~~$0.5~~$1.4 million from $4.4 million during the three months ended ~~March 31,~~September 30, 2019 to ~~$4.9~~$5.9 million during the three months ended ~~March 31,~~September 30, 2020. The increase in general and administrative expense was primarily attributable to the following:

•an increase of $0.9 million related to consulting and professional fees;

•an increase of $0.3 million related to employee compensation, primarily due to the increase in ~~the~~ valuation of stock-based awards granted to employees, resulting in higher ~~stock~~stock-based compensation ~~expense.~~

expense; and

•an increase of $0.2 million in facility-related costs as a result of the amendment of our lease in March 2020.

We expect that our general and administrative expense will increase in future periods as we expand our ~~operations~~.operations. These increases will likely include legal, auditing and filing fees, additional insurance premiums and general compliance and consulting expenses.

Total Other Income (Expense), net

Total other income (expense), net was ~~$0.2~~$0.1 million and $0.5 million for the three months ended ~~March 31,~~September 30, 2020 and 2019, respectively. Other income consists primarily of interest income on cash equivalents and short-term marketable ~~securities, which decreased $0.1 million due~~securities. Interest expense related to ~~lower investable balances~~our outstanding borrowings under the credit facility.

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Comparison of the nine months ended September 30, 2020 and 2019

The following table summarizes our results of operations for the ~~three~~nine months ended ~~March 31, 2020. Interest expense~~September 30, 2020 and 2019:


	Nine Months Ended September 30,				Dollar Change
(in thousands)	2020		2019
Collaboration revenue	$	817	$	42,081	$	(41,264)
Operating expenses:
Research and development	44,179		42,610		1,569
General and administrative	15,988		13,072		2,916
Total operating expenses	60,167		55,682		4,485
Other income (expense):
Interest income	414		1,785		(1,371)
Interest expense	(267)		(146)		(121)
Total other income (expense), net	147		1,639		(1,492)
Net income (loss)	$	(59,203)	$	(11,962)	$	(47,241)

Collaboration Revenue

Collaboration revenue was $0.8 million during the nine months ended September 30, 2020 and $42.1 million during the nine months ended September 30, 2019. The decrease in collaboration revenue was primarily a result of ~~$0.1~~the termination of the Takeda agreements and the recognition of the remaining deferred revenue of $40.0 million in the first quarter of 2019. During the nine months ended September 30, 2020 revenue of $0.8 million was recognized as a result of completion of research services associated with a target included in the Merck KGaA Agreement. Additionally, during the nine months ended September 30, 2019, collaboration revenue of $1.0 million was recognized related to the Merck KGaA Agreement and Merck KGaA Supply Agreement.

Research and Development Expense

Research and development expense increased by $1.6 million from $42.6 million for the nine months ended September 30, 2019 to $44.2 million for the nine months ended September 30, 2020.

The increase in research and development expense was primarily attributable to the following:

•an increase of $3.7 million related to manufacturing, clinical and regulatory activities for XMT-1536;

•an increase of $1.8 million related to employee compensation, primarily due to increased headcount supporting the growth of our research and development activities, and the increase in valuation of stock-based awards granted to employees, resulting in higher stock-based compensation expense;

•an increase of $1.3 million related to XMT-1592 clinical and regulatory expenses;

•an increase of $0.8 million related to consulting and professional fees;

•an increase of $0.7 million related to advancement of companion diagnostic development efforts for the NaPi2B biomarker;

•an increase of $0.6 million related to manufacturing activities for our discovery stage programs; and

•an increase of $0.4 million related to a milestones paid for in-licensed technologies.

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These increased costs were partially offset by the following:

•a decrease of $4.8 million related to preclinical development and manufacturing activities for XMT-1592;

•a decrease of $2.0 million related to the development and manufacturing activities for XMT-1522; and

•a decrease of $0.9 million to support partner programs.

General and Administrative Expense

General and administrative expense increased by $2.9 million from $13.1 million during the nine months ended September 30, 2019 to $16.0 million during the nine months ended September 30, 2020. The increase in general and administrative was primarily attributable to the following:

•an increase of $1.6 million related to consulting and professional fees;

•an increase of $1.0 million related to employee compensation, primarily due to the increase in valuation of stock-based awards granted to employees, resulting in higher stock-based compensation expense; and

•an increase of $0.3 million in facility-related costs as a result of the amendment of our lease in March 2020.

We expect that our general and administrative expense will increase in future periods as we expand our operations. These increases will likely include legal, auditing and filing fees, additional insurance premiums and general compliance and consulting expenses.

Total Other Income (Expense), net

Total other income (expense), net was $0.1 million and $1.6 million for the nine months ended September 30, 2020 and 2019, respectively. Other income consists primarily of interest income on cash equivalents and short-term marketable securities. Interest expense was related to our outstanding borrowings under the credit facility.

Liquidity and Capital Resources

Sources of Liquidity

Since our initial public offering in July 2017, we have financed our operations primarily with the proceeds from ~~that~~our initial public offering, ~~and~~ our ~~2019~~ follow-on public ~~offering. The~~offerings and use of our at-the-market, or ATM, equity offering program established in July 2018. We completed a follow-on public offering ~~was completed~~ on March 5, 2019 ~~and~~that resulted in net proceeds of $92.2 million. On May 8, 2019, ~~the Company~~we entered into a term-loan agreement ~~for~~which was subsequently amended on August 28, 2020. Pursuant to the amendment, we may be subject to certain conditions, borrow term loans in an aggregate amount of up to ~~$20.0~~$30.0 million, of which ~~$5.0~~$5.2 million ~~was~~were funded ~~in connection with the~~ upon execution of the ~~agreement.~~amendment. These proceeds were used to repay the existing balance and satisfy our existing obligations to Silicon Valley Bank, or SVB. No additional amounts have been drawn since the initial ~~$5.0~~draw of $5.2 million. ~~As of March 31,~~

In April 2020, we ~~had cash, cash equivalents~~sold approximately 10.9 million shares of common stock and ~~marketable securities~~received net proceeds of ~~$78.4~~$63.0 million pursuant to our 2018 ATM. In addition, in June 2020, we sold 9.2 million shares of common stock in a follow-on offering and received net proceeds of approximately $164.0 million.

We terminated the 2018 ATM on April 9, 2020. On ~~July 2, 2018,~~May 8, 2020, we established ana new ATM pursuant to which we are able to ~~offer and~~ sell ~~up to $75.0~~$100.0 million of our common stock from time to time at prevailing market ~~prices.~~ prices, or the 2020 ATM.

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As of ~~March 31,~~September 30, 2020, we had not sold any shares under the 2020 ATM and had ~~$75.0~~$100.0 million of availability under the program. ~~On April 7,~~

As of September 30, 2020, we ~~sold 8.9 million~~had cash and ~~2.0 million shares~~cash equivalents of ~~common stock at$5.59 per share and $7.74 per share, respectively, to raise gross proceeds of approximately $65~~$270.9 million.

Cash Flows

The following table provides information regarding our cash flows for the ~~three~~nine months ended ~~March 31,~~September 30, 2020 and 2019:


	Three months ended
	March 31,					Nine Months Ended September 30,
(in thousands)	2020		2019		(in thousands)	2020		2019
Net cash used in operating activities	$	(21,246)	$	(24,687)	Net cash used in operating activities	$	(57,377)	$	(55,168)
Net cash provided by investing activities		19,435		10,128
Net cash provided by (used in) financing activities		(90)		92,204
Net cash provided by (used in) investing activities					Net cash provided by (used in) investing activities	37,215		(43,793)
Net cash provided by financing activities					Net cash provided by financing activities	228,747		97,473
Increase (decrease) in cash, cash equivalents and restricted cash	$	(1,901)	$	77,645	Increase (decrease) in cash, cash equivalents and restricted cash	$	208,585	$	(1,488)

Net Cash Used in Operating Activities

Net cash used in operating activities was ~~$21.2~~$57.4 million for the ~~three~~nine months ended ~~March 31,~~September 30, 2020 and primarily consisted of a net loss of ~~$16.9~~$59.2 million adjusted for changes in our net working capital and other non-cash items including stock-based compensation of ~~$1.6~~$5.2 million and depreciation of ~~$0.2~~$0.8 million. Net cash used in operating activities was ~~$24.7~~$55.2 million for the ~~three~~nine months ended ~~March 31,~~September 30, 2019 and primarily consisted of a net ~~income~~loss of ~~$21.9~~$12.0 million adjusted for non-cash items including the decrease in deferred revenue of ~~$41.0~~$41.6 million primarily related to the Takeda agreements, stock-based compensation of ~~$1.2~~$3.6 million and depreciation of ~~$0.3~~$1.0 million, as well as change in our net working capital.

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Net Cash Provided by (Used in) Investing Activities

Net cash provided by investing activities was ~~$19.4 million and $10.1~~$37.2 million during the ~~three~~nine months ended ~~March 31,~~September 30, 2020 ~~and 2019, respectively,~~ and consisted primarily of maturities of marketable securities.

Net cash used in investing activity was $43.8 million during the nine months ended September 30, 2019 and consisted primarily of purchases of marketable securities, slightly offset by the maturity of marketable securities.

Net Cash Provided by ~~(Used in)~~ Financing Activities

Net cash ~~used in~~provided by financing activities was ~~$0.1~~$228.7 million during the ~~three~~nine months ended ~~March 31,~~September 30, 2020 as compared to net cash provided by financing activities of ~~$92.2~~$97.5 million during the ~~three~~nine months ended ~~March 31,~~September 30, 2019. During the ~~three~~nine months ended ~~March 31,~~September 30, 2020 cash ~~used in~~provided by financing activities consisted primarily of $164.0 million related to the follow-on public offering in May 2020 and the proceeds from the use of the ATM of $63.0 million in April 2020 as well as proceeds from exercise of stock options of $1.7 million, offset by the payment of $0.2 million of ~~debt issuance costs, offset by $0.1 million in proceeds from the exercise of stock options.~~debt. During the ~~three~~nine months ended ~~March 31,~~September 30, 2019 cash provided by financing activities consisted primarily of the proceeds from ~~the Company’s~~our follow-on public offering.

Funding Requirements

We expect our cash expenditures to increase in connection with our ongoing activities, particularly as we continue the research and development of, initiate clinical studies of, and seek marketing approval for our product candidates. In addition, if we obtain marketing approval for any of our product candidates, we expect to incur significant commercialization expenses related to drug sales, marketing, manufacturing and distribution to the extent that such sales, marketing and distribution are not the responsibility of potential collaborators.

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We believe our currently available funds will be sufficient to fund our existing cash flow requirements and our ~~operations at their currently planned levels through at least the twelve months following the filing of this Quarterly Report on Form 10-Q~~.current operating plan commitments for more than two years. Our forecast of the period of time through which our financial resources will be adequate to support our operations is a forward-looking statement and involves risks and uncertainties, and actual results could vary as a result of a number of factors. We have based this estimate on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect. Our future capital requirements will depend on many factors, including:

~~the scope, progress, results and costs of drug discovery, preclinical development, laboratory testing and clinical studies for our product candidates;~~

~~the scope, prioritization and number of our research and development programs;~~

•the scope, progress, results and costs of drug discovery, preclinical development, laboratory testing and clinical studies for our product candidates;

~~the costs, timing and outcome of regulatory review of our product candidates;~~

•the scope, prioritization and number of our research and development programs;

~~our ability to establish and maintain collaborations on favorable terms, if at all;~~

•the costs, timing and outcome of regulatory review of our product candidates;

~~the achievement of milestones or occurrence of other developments that trigger payments under any collaboration agreements we obtain;~~

•our ability to establish and maintain collaborations on favorable terms, if at all;

~~the extent to which we are obligated to reimburse, or entitled to reimbursement of, clinical study costs under future collaboration agreements, if any;~~

•the achievement of milestones or occurrence of other developments that trigger payments under any collaboration agreements we obtain;

~~the costs of preparing, filing and prosecuting patent applications, maintaining and enforcing our intellectual property rights and defending intellectual property‑related claims;~~

•the extent to which we are obligated to reimburse, or entitled to reimbursement of, clinical study costs under future collaboration agreements, if any;

~~the extent to which we acquire or in‑license other product candidates and technologies;~~

•the costs of preparing, filing and prosecuting patent applications, maintaining and enforcing our intellectual property rights and defending intellectual property-related claims;

~~the costs of securing manufacturing arrangements for clinical and commercial production; and~~

•the extent to which we acquire or in-license other product candidates and technologies;

~~the costs of establishing or contracting for sales and marketing capabilities if we obtain regulatory approvals to market our product candidates.~~

•the costs of securing manufacturing arrangements for clinical and commercial production; and

•the costs of establishing or contracting for sales and marketing capabilities if we obtain regulatory approvals to market our product candidates.

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Identifying potential product candidates and conducting preclinical testing and clinical studies is a ~~time‑consuming,~~time-consuming, expensive and uncertain process that takes many years to complete, and we may never generate the necessary data or results required to obtain marketing approval and achieve drug sales. In addition, our product candidates, if approved, may not achieve commercial success. Our commercial revenues, if any, will be derived from sales of drugs that we do not expect to be commercially available for many years, if at all. Accordingly, we will need to continue to rely on additional financing to achieve our business objectives. Adequate additional financing may not be available to us on acceptable terms, or at all.

Until such time, if ever, as we can generate substantial product revenues, we expect to finance our cash needs through a combination of equity offerings, debt financings, strategic partnerships and licensing arrangements. To the extent that we raise additional capital through the sale of equity or convertible debt securities, the ownership interests of our common stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of our common stockholders. We have access to an additional line of credit ~~of $15.0 million~~ under the ~~Credit Facility~~credit facility with SVB, along with funds to be earned in connection with our agreements with Merck KGaA and Asana BioSciences, if development activities are successful under those agreements. Future additional debt financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends.

If we raise funds through additional strategic partnerships or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs or product candidates or to grant licenses on terms that may not be favorable to us. If we are unable to raise additional funds through equity or debt financings when needed, we may be required to delay, limit, reduce or terminate our drug development or

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future commercialization efforts or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.

~~Off‑Balance~~

Off-Balance Sheet Arrangements

We did not have, during the periods presented, and we do not currently have, any ~~off‑balance~~off-balance sheet arrangements, as defined under applicable Securities and Exchange Commission rules.

Critical accounting policies and significant judgments and estimates

Our management's discussion and analysis of our financial condition and results of operations are based on our financial statements, which have been prepared in accordance with U.S. generally accepted accounting principles. The preparation of these financial statements requires us to make judgments and estimates that affect the reported amounts of assets, liabilities, revenues, and expenses and the disclosure of contingent assets and liabilities in our financial statements. We base our estimates on historical experience, known trends and events, and various other factors that are believed to be reasonable under the circumstances. Actual results may differ from these estimates under different assumptions or conditions. On an ongoing basis, we evaluate our judgments and estimates in light of changes in circumstances, facts and experience. The effects of material revisions in estimates, if any, will be reflected in the financial statements prospectively from the date of change in estimates. There were no material changes to our critical accounting policies as reported in our Annual Report on Form 10-K for the year ended December 31, 2019, which was filed with the SEC on February 28, 2020.

Item 3. Quantitative and Qualitative Disclosures About Market Risk

We are exposed to market risk-related to changes in interest rates. Our primary exposure to market risk is interest rate sensitivity, which is affected by changes in the general level of U.S. interest rates, particularly because our investments, including cash equivalents and marketable securities are invested in U.S. Treasury obligations, commercial paper and corporate bonds. However, we believe that due to the short-term duration of our investment portfolio and low-risk profile of our investments, an immediate 100 basis points change in interest rates would not have a material effect on the fair market value of our investments portfolio.

We are currently not exposed to market risk related to changes in foreign currency exchange rates, but we may contract with vendors that are located in Asia and Europe and may be subject to fluctuations in foreign currency rates at that time.

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Item 4. Controls and Procedures

Management’s Evaluation of our Disclosure Controls and Procedures

We maintain “disclosure controls and procedures,” as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended ~~(Exchange~~(the Exchange Act), that are designed to ensure that information required to be disclosed in the reports that we file or submit under the Exchange Act is (i) recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms and (ii) accumulated and communicated to our management, including our principal executive and principal financial officer, as appropriate to allow timely decisions regarding required disclosure. 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 our management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Our disclosure controls and procedures are designed to provide reasonable assurance of achieving their control objectives.

Our management, with the participation of our principal executive officer and principal financial officer, has evaluated the effectiveness of our disclosure controls and procedures as of ~~March 31,~~September 30, 2020, the end of the period covered by this Quarterly Report on Form 10-Q. Based upon such evaluation, our principal executive officer and principal financial officer have concluded that our disclosure controls and procedures were effective at the reasonable assurance level as of such date.

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Changes in Internal Control over Financial Reporting

There was no change in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) that occurred during the ~~three months~~quarter ended ~~March 31,~~September 30, 2020 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

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PART II - OTHER INFORMATION

Item 1. Legal Proceedings

From time to time, we may be subject to various legal proceedings and claims that arise in the ordinary course of our business activities. Although the results of litigation and claims cannot be predicted with certainty, as of the date of this Quarterly Report on Form 10-Q, we do not believe we are party to any claim or litigation, 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. Regardless of the outcome, litigation can have an adverse impact on us because of defense and settlement costs, diversion of management resources and other factors.

Item 1A. Risk Factors

Risk Factors

~~Other than as disclosed below, there~~

There have been no material changes to the Company’s risk factors as set forth in Part I, Item 1A of the Company’s Annual Report on Form 10-K, as filed with the SEC on February 28, ~~2020.~~

~~Our business is subject to risks arising from~~2020, other than those set forth in "Part II, Item 1A—Risk Factors" in our Quarterly Report on Form 10-Q for the ~~outbreaks of disease, such~~quarterly period ended March 31, 2020, as ~~epidemics or pandemics, including~~filed with the ~~ongoing COVID-19 pandemic.~~

On January 30, 2020, the World Health Organization (the “WHO”) announced a global health emergency because of COVID-19, the strain of novel coronavirus that originated in Wuhan, China and has since spread globally. In March 2020, the WHO declared the COVID-19 outbreak a pandemic and recommended containment and mitigation measures worldwide. On March 13, 2020, President Trump announced a National Emergency relating to the disease. The widespread infection in the United States and abroad has caused significant volatility and uncertainty in U.S. and international markets, which could result in a prolonged economic downturn that may disrupt the Company’s business, including by adversely affecting our ability to conduct financingsSEC on ~~terms acceptable to us, if at all.~~

~~In addition, we may experience disruptions that could severely impact our business, preclinical studies and clinical trials, including:~~

Our clinical trials may be adversely affected, delayed or interrupted, including, for example, site initiation, patient recruitment and enrollment, availability of clinical trial materials, and data analysis. Some patients and clinical investigators may not be able to comply with clinical trial protocols and patients may choose to withdraw from our studies or we may have to pause enrollment or we may choose to or be required to pause enrollment and or patient dosing in our ongoing clinical trials in order to preserve health resources and protect trial participants. It is unknown how long these pauses or disruptions could continue.

May 8, 2020.

We currently rely on third parties to, among other things, manufacture raw materials, manufacture our product candidates for our clinical trials, shipping of investigation drugs and clinical trial samples, perform quality testing and supply other goods and services to run our business. If any such third party in our supply chain for materials are adversely impacted by restrictions resulting from the coronavirus pandemic, including staffing shortages, production slowdowns and disruptions in delivery systems, our supply chain may be disrupted, limiting our ability to manufacture our product candidates for our clinical trials and conduct our research and development operations.

We have requested that most of our personnel work remotely, restricted on-site staff to only those personnel and contractors who must perform essential activities that must be completed on-site and limited the number of staff in any given research and development laboratory. Our increased reliance on personnel working from home may negatively impact productivity, or disrupt, delay, or otherwise adversely impact our business. In addition, this 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 or delay necessary interactions with local and federal regulators, ethics committees, manufacturing sites, research or clinical trial sites and other important agencies and contractors.

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Our employees and contractors conducting research and development activities may not be able to access our laboratory for an extended period of time as a result of the closure of our offices and the possibility that governmental authorities further modify current restrictions. As a result, this could delay timely completion of preclinical activities, including completing Investigational New Drug (IND)-enabling studies or our ability to select future development candidates, and initiation of additional clinical trials for other of our development programs.

Health regulatory agencies globally may experience disruptions in their operations as a result of the coronavirus pandemic. The U.S. Food and Drug Administration, or FDA, and comparable foreign regulatory agencies may have slower response times or be under-resourced to continue to monitor our clinical trials and, as a result, review, inspection, and other timelines may be materially delayed. It is unknown how long these disruptions could continue, were they to occur. Any prolongation or de-prioritization of our clinical trials or delay in regulatory review resulting from such disruptions could materially affect the development and study of our product candidates. For example, regulatory authorities may require that we not distribute a product candidate lot until the relevant agency authorizes its release. Such release authorization may be delayed as a result of the coronavirus pandemic and could result in delays to our clinical trials.

The trading prices for our common shares and other biopharmaceutical companies have been highly volatile as a result of the coronavirus pandemic. As a result, we may face difficulties raising capital through sales of our common shares or such sales may be on unfavorable terms. In addition, a recession, depression or other sustained adverse market event resulting from the spread of the coronavirus could materially and adversely affect our business and the value of our common shares.

The coronavirus pandemic continues to evolve, rapidly. The ultimate impact of the coronavirus pandemic on our business operations is highly uncertain and subject to change and will depend on future developments, which cannot be accurately predicted, including the duration of the pandemic, the ultimate geographic spread of the disease, additional or modified government actions, new information that will emerge concerning the severity and impact of COVID-19 and the actions taken to contain coronavirus or address its impact in the short and long term, among others. We do not yet know the full extent of potential delays or impacts on our business, our clinical trials, our research programs, healthcare systems or the global economy.

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Item 6. Exhibits.


EXHIBIT 3.1			-		Fifth Amended and Restated Certificate of Incorporation (incorporated by reference to Exhibit 3.1 to the Company’s Current Report on Form 8-K, filed on July 10, 2017).

EXHIBIT 3.2			-		Amended and Restated Bylaws (incorporated by reference to Exhibit 3.2 to the Company’s Current Report on Form 8-K, filed on July 10, 2017).

EXHIBIT 10.1			-		~~Seventh Lease Extension~~Second Amendment to Loan and ~~Modification~~Security Agreement, ~~to the Lease Between Rivertech Associates II LLC and Mersana Therapeutics, Inc.~~ dated ~~March 10~~August 28, 2020, by and between Mersana Therapeutics, Inc., and ~~Rivertech Associates II LLC.~~Silicon Valley Bank (incorporated by reference to Exhibit 10.1 to the Company’s Current Report on Form 8-K, filed on September 3,2020).

~~EXHIBIT 10.2~~			-	~~Offer Letter, by and between Mersana Therapeutics, Inc. and Dirk Huebner, dated November 5, 2018.~~

~~EXHIBIT 10.3~~	-	~~Offer Letter, by and between Mersana Therapeutics, Inc. and Brian DeSchuytner, dated June 10, 2019.~~

EXHIBIT 31.1	-			Rule 13a—14(a) / 15d—14(a) Certifications — Chief Executive Officer.

EXHIBIT 31.2			-		Rule 13a—14(a) / 15d—14(a) Certifications — Principal Financial Officer.

EXHIBIT 32.1			-		Section 1350 Certifications.

EXHIBIT ~~101.INS~~ 101			-		~~XBRL Instance Document.~~ The following financial and related information from Mersana Therapeutics, Inc.’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2020, formatted in Inline eXtensible Business Reportable Language (iXBRL) includes: (i) the Condensed Consolidated Balance Sheet; (ii) the Condensed Consolidated Statement of Operations and Comprehensive Income (Loss); (iii) the Condensed Consolidated Statement of Changes in Stockholders' Equity; (iv) the Condensed Consolidated Statement of Cash Flows; and, (v) Notes to Condensed Consolidated Financial Statements.

EXHIBIT ~~101.SCH~~ 104			-		The cover page from the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2020, formatted in Inline XBRL ~~Taxonomy Extension Schema Document.~~

~~EXHIBIT 101.CAL~~	-	~~XBRL Taxonomy Extension Calculation Linkbase Document.~~

~~EXHIBIT 101.DEF~~	-	~~XBRL Taxonomy Extension Definition Linkbase Document.~~

~~EXHIBIT 101.LAB~~	-	~~XBRL Taxonomy Extension Label Linkbase Document.~~

~~EXHIBIT 101.PRE~~	-	~~XBRL Taxonomy Extension Presentation Linkbase Document.~~ (contained in Exhibit 101).

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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.


		Mersana Therapeutics, Inc.

Dated: ~~May 8,~~November 9, 2020		By:	/s/ Anna Protopapas
			Anna Protopapas
	President and Chief Executive Officer

Dated: ~~May 8,~~November 9, 2020		By:	/s/ Brian DeSchuytner
			Brian DeSchuytner
	Senior Vice President, Finance & Product Strategy


	Three months ended
	March 31,					Nine Months Ended September 30,
	2020		2019			2020		2019
Cash flows from operating activities					Cash flows from operating activities
Net income (loss)	$	(16,926)	$	21,901
Adjustments to reconcile net income (loss) to net cash used in operating activities:
Net loss					Net loss	$	(59,203)	$	(11,962)
Adjustments to reconcile net loss to net cash used in operating activities:					Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation		248		337	Depreciation	750		963

Net amortization of premiums and discounts on investments		(66)		4	Net amortization of premiums and discounts on investments	(86)		(87)
Stock-based compensation		1,609		1,164	Stock-based compensation	5,183		3,610

Other non-cash items		37		26	Other non-cash items	110		65
Changes in operating assets and liabilities:					Changes in operating assets and liabilities:
Accounts receivable		—		(9)	Accounts receivable	0		161
Prepaid expenses and other current assets		(330)		389	Prepaid expenses and other current assets	(2,460)		1,318
Other assets					Other assets	(700)		0
Accounts payable		(2,693)		(3,444)	Accounts payable	(2,766)		(3,102)
Accrued expenses		(3,128)		(4,463)	Accrued expenses	2,367		(4,518)
Operating lease assets		444		—	Operating lease assets	1,235		1,290
Operating lease liabilities		(430)		—	Operating lease liabilities	(990)		(1,356)
Deferred revenue		(11)		(40,592)	Deferred revenue	(817)		(41,550)
Net cash used in operating activities		(21,246)		(24,687)	Net cash used in operating activities	(57,377)		(55,168)

Cash flows from investing activities					Cash flows from investing activities
Maturities of marketable securities		19,500		10,500	Maturities of marketable securities	37,500		10,500
Purchase of marketable securities					Purchase of marketable securities	0		(53,688)
Purchase of property and equipment		(65)		(372)	Purchase of property and equipment	(285)		(605)
Net cash provided by investing activities		19,435		10,128
Net cash provided by (used in) investing activities					Net cash provided by (used in) investing activities	37,215		(43,793)

Cash flows from financing activities					Cash flows from financing activities
Net proceeds from public offering of common stock		—		92,162	Net proceeds from public offering of common stock	163,990		92,162
Net proceeds from the at-the-market (ATM) facility					Net proceeds from the at-the-market (ATM) facility	62,976		0
Proceeds from exercise of stock options		119		42	Proceeds from exercise of stock options	1,732		121
Payments from issuance of debt		(180)		—
Proceeds from purchases of common stock under ESPP					Proceeds from purchases of common stock under ESPP	333		283
Proceeds from issuance of debt, net of issuance costs					Proceeds from issuance of debt, net of issuance costs	(197)		4,965

Payments under capital lease obligations		(29)		—	Payments under capital lease obligations	(87)		(58)
Net cash provided by (used in) financing activities		(90)		92,204
Net cash provided by financing activities					Net cash provided by financing activities	228,747		97,473

Increase (decrease) in cash, cash equivalents and restricted cash		(1,901)		77,645	Increase (decrease) in cash, cash equivalents and restricted cash	208,585		(1,488)
Cash, cash equivalents and restricted cash, beginning of period		62,672		60,005	Cash, cash equivalents and restricted cash, beginning of period	62,672		60,005
Cash, cash equivalents and restricted cash, end of period	$	60,771	$	137,650	Cash, cash equivalents and restricted cash, end of period	$	271,257	$	58,517

Supplemental disclosures of non-cash activities:					Supplemental disclosures of non-cash activities:
Purchases of property and equipment in accounts payable and accrued expenses	$	—	$	26

Debt financing costs in accrued expenses					Debt financing costs in accrued expenses	$	0	$	180

Cash paid for interest	$	56	$	—	Cash paid for interest	$	173	$	64
Right-of-use assets obtained in exchange for operating lease liabilities	$	9,980	$	4,369	Right-of-use assets obtained in exchange for operating lease liabilities	$	9,980	$	4,778
Right-of-use assets obtained in exchange for financing lease liabilities	$	—	$	429	Right-of-use assets obtained in exchange for financing lease liabilities	$	0	$	429


	March 31,		December 31,
	2020		2019			September 30, 2020		December 31, 2019
Accrued payroll and related expenses	$	1,549	$	4,037	Accrued payroll and related expenses	$	3,647	$	4,037
Accrued preclinical, manufacturing and clinical expenses		3,367		4,230	Accrued preclinical, manufacturing and clinical expenses	6,600		4,230
Accrued professional fees		716		675
Accrued professional fees and insurance					Accrued professional fees and insurance	861		675
Accrued other		46		44	Accrued other	65		44
	$	5,678	$	8,986		$	11,173	$	8,986


		Weighted-
	Number	Average
	of Shares	Exercise Price
					Number of Shares	Weighted- Average Exercise Price
Outstanding at January 1, 2020	4,720,772	$	5.24	Outstanding at January 1, 2020	4,720,772	$	5.24
Granted	1,412,653		6.10	Granted	1,960,374	9.41
Exercised	(43,055)		2.77	Exercised	(338,069)	5.13
Cancelled	(41,082)		8.50	Cancelled	(127,709)	7.70
Outstanding at March 31, 2020	6,049,288	$	5.44

Exercisable at March 31, 2020	2,846,100	$	4.68
Outstanding at September 30, 2020				Outstanding at September 30, 2020	6,215,368	$	6.52
Exercisable at September 30, 2020				Exercisable at September 30, 2020	3,256,514	$	4.87


	Operating leases		Finance leases			Operating leases		Finance leases
2020 (excluding the three months ended March 31, 2020)	$	1,809	$	87
2020 (excluding the nine months ended September 30, 2020)					2020 (excluding the nine months ended September 30, 2020)	$	604	$	29
2021		2,772		116	2021	2,772		116
2022		2,843		84	2022	2,843		84
2023		2,928		74	2023	2,928		74
2024 and thereafter		6,904		18	2024 and thereafter	6,904		18
Total lease payments		17,256		379	Total lease payments	16,051		321
Present value adjustment		(4,811)		(41)	Present value adjustment	(4,165)		(30)
Present value of lease liabilities	$	12,445	$	338	Present value of lease liabilities	$	11,886	$	291



				Additional		Accumulated
	Common Stock			Paid-in		Other Comprehensive		Accumulated		Stockholders’			Common Stock			Additional Paid-in Capital				Accumulated Other Comprehensive Income (Loss)		Accumulated Deficit		Stockholders’ Equity
	Shares	Amount		Capital		Income (Loss)		Deficit		Equity			Shares	Amount
Balance at December 31, 2018	23,234,472	$	3	$	172,966	$	(8)	$	(164,166)	$	8,795	Balance at December 31, 2018	23,234,472	$	3			$	172,966			$	(8)	$	(164,166)	$	8,795
Exercise of stock options	12,192		—		42		—		—		42	Exercise of stock options	12,192	—		42				—		—		42
Issuance of common stock under public offering, net of issuance costs of $5,587	24,437,500		2		92,160		—		—		92,162	Issuance of common stock under public offering, net of issuance costs of $5,587	24,437,500	2		92,160				—		—		92,162
Stock-based compensation expense	—		—		1,164		—		—		1,164	Stock-based compensation expense	—	—		1,164				—		—		1,164
Other comprehensive income	—		—		—		8		—		8	Other comprehensive income	—	—		—				8		—		8
Net income	—		—		—		—		21,901		21,901	Net income	—	—		—				—		21,901		21,901
Balance at March 31, 2019	47,684,164		5		266,332		—		(142,265)		124,072	Balance at March 31, 2019	47,684,164	$	5	$	266,332			$	—	$	(142,265)	$	124,072
Exercise of stock options	32,693		—		58		—		—		58	Exercise of stock options	32,693	—		58				—		—		58
Purchase of common stock under ESPP	82,281		—		283		—		—		283	Purchase of common stock under ESPP	82,281	—		283				—		—		283
Stock-based compensation expense	—		—		1,161		—		—		1,161	Stock-based compensation expense	—	—		1,161				—		—		1,161
Other comprehensive income	—		—		—		11		—		11	Other comprehensive income	—	—		—				11		—		11
Net loss	—		—		—		—		(17,071)		(17,071)	Net loss	—	—		—				—		(17,071)		(17,071)
Balance at June 30, 2019	47,799,138		5		267,834		11		(159,336)		108,514	Balance at June 30, 2019	47,799,138	$	5	$	267,834			$	11	$	(159,336)	$	108,514
Exercise of stock options and warrants	83,759		—		21		—		—		21	Exercise of stock options and warrants	83,759	—		21				—		—		21
Stock-based compensation expense	—		—		1,285		—		—		1,285	Stock-based compensation expense	—	—		1,285				—		—		1,285
Other comprehensive income	—		—		—		17		—		17	Other comprehensive income	—	—		—				17		—		17
Net loss	—		—		—		—		(16,792)		(16,792)	Net loss	—	—		—				—		(16,792)		(16,792)
Balance at September 30, 2019	47,882,897		5		269,140		28		(176,128)		93,045	Balance at September 30, 2019	47,882,897	$	5	$	269,140			$	28	$	(176,128)	$	93,045
Retirement of common stock in exchange for common stock warrant	(2,575,000)		—		(8,986)		—		—		(8,986)	Retirement of common stock in exchange for common stock warrant	(2,575,000)	—		(8,986)				—		—		(8,986)
Issuance of common stock warrant in exchange for retirement of common stock	—		—		8,986		—		—		8,986	Issuance of common stock warrant in exchange for retirement of common stock	—	—		8,986				—		—		8,986
Purchase of common stock under ESPP	57,792		—		206		—		—		206	Purchase of common stock under ESPP	57,792	—		206				—		—		206
Exercise of stock options and warrants	22,334		—		54		—		—		54	Exercise of stock options and warrants	22,334	—		54				—		—		54
Stock-based compensation expense	—		—		1,262		—		—		1,262	Stock-based compensation expense	—	—		1,262				—		—		1,262
Other comprehensive loss	—		—		—		(3)		—		(3)	Other comprehensive loss	—	—		—				(3)		—		(3)
Net loss	—		—		—		—		(16,246)		(16,246)	Net loss	—	—		—				—		(16,246)		(16,246)
Balance at December 31, 2019	45,388,023		5		270,662		25		(192,374)		78,318	Balance at December 31, 2019	45,388,023	$	5	$	270,662			$	25	$	(192,374)	$	78,318
Exercise of common stock warrant in exchange for common stock	2,574,971		—		—		—		—		—	Exercise of common stock warrant in exchange for common stock	2,574,971	—		—				—		—		0
Exercise of stock options and warrants	43,055		—		119		—		—		119
Exercise of stock options												Exercise of stock options	43,055	—		119				—		—		119
Stock-based compensation expense	—		—		1,609		—		—		1,609	Stock-based compensation expense	—	—		1,609				—		—		1,609
Other comprehensive loss	—		—		—		(29)		—		(29)	Other comprehensive loss	—	—		—				(29)		—		(29)
Net loss	—		—		—		—		(16,926)		(16,926)	Net loss	—	—		—				—		(16,926)		(16,926)
Balance at March 31, 2020	48,006,049	$	5	$	272,390	$	(4)	$	(209,300)	$	63,091	Balance at March 31, 2020	48,006,049	$	5	$	272,390			$	(4)	$	(209,300)	$	63,091
Issuance of common stock from at-the-market transactions, net of issuance costs of $2,176												Issuance of common stock from at-the-market transactions, net of issuance costs of $2,176	10,900,599	1		62,976				—		—		62,977
Issuance of common stock under public offering, net of issuance costs of $10,809												Issuance of common stock under public offering, net of issuance costs of $10,809	9,200,000	1		163,990				—		—		163,991
Purchase of common stock under ESPP												Purchase of common stock under ESPP	68,419	—		333				—		—		333
Exercise of stock options												Exercise of stock options	206,143	—		1,296				—		—		1,296
Stock-based compensation expense												Stock-based compensation expense	—	—		1,656				—		—		1,656
Other comprehensive income												Other comprehensive income	—	—		—				6		—		6
Net loss												Net loss	—	—		—				—		(19,786)		(19,786)
Balance at June 30, 2020												Balance at June 30, 2020	68,381,210	$	7	$	502,641			$	2	$	(229,086)	$	273,564
Exercise of stock options												Exercise of stock options	88,871	—		317				—		—		317
Stock-based compensation expense												Stock-based compensation expense	—	—		1,918				—		—		1,918
Other comprehensive loss												Other comprehensive loss	—	—		—				(2)		—		(2)
Net loss												Net loss	—	—		—				—		(22,489)		(22,489)
Balance at September 30, 2020												Balance at September 30, 2020	68,470,081	$	7	$	504,876			$	0	$	(251,575)	$	253,308


	Three months ended				Three months ended
	March 31, 2020				March 31, 2019
	Beginning		End		Beginning		End			Nine Months Ended September 30, 2020				Nine Months Ended September 30, 2019
	of period		of period		of period		of period			Beginning of period		End of period		Beginning of period		End of period
Cash and cash equivalents	$	62,351	$	60,450	$	59,634	$	137,279	Cash and cash equivalents	$	62,351	$	270,936	$	59,634	$	58,196
Restricted cash included in other assets, noncurrent		321		321		371		371	Restricted cash included in other assets, noncurrent	321		321		371		321
Total cash, cash equivalents and restricted cash per statement of cash flows	$	62,672	$	60,771	$	60,005	$	137,650	Total cash, cash equivalents and restricted cash per statement of cash flows	$	62,672	$	271,257	$	60,005	$	58,517


	Balance at									Balance at Beginning of Period		Additions		Deductions		Balance at End of Period
	Beginning						Balance at
	of Period		Additions		Deductions		End of Period
Three months ended March 31, 2020
Nine months ended September 30, 2020									Nine months ended September 30, 2020
Contract assets	$	—	$	—	$	—	$	—	Contract assets	$	0	$	—	$	—	$	0
Contract liabilities:									Contract liabilities:
Deferred revenue	$	4,815	$	—	$	11	$	4,804	Deferred revenue	$	4,815	$	0	$	817	$	3,998

	Balance at
	Beginning						Balance at
	of Period		Additions		Deductions		End of Period
Three months ended March 31, 2019
Contract assets	$	—	$	—	$	—	$	—
Contract liabilities:
Deferred revenue	$	46,196	$	—	$	40,592	$	5,604


					Significant					Fair Value		Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
			Quoted Prices		Other		Significant
			in Active		Observable		Unobservable
	Fair		Markets		Inputs		Inputs
	Value		(Level 1)		(Level 2)		(Level 3)
March 31, 2020
December 31, 2019									December 31, 2019
Marketable securities:									Marketable securities:
Commercial paper	$	5,983	$	—	$	5,983	$	—	Commercial paper	$	11,940	$	0	$	11,940	$	0
Corporate bonds		11,993		—		11,993		—	Corporate bonds	12,010		0		12,010		0
U.S. Treasuries									U.S. Treasuries	13,489		13,489		0		0
	$	17,976	$	—	$	17,976	$	—		$	37,439	$	13,489	$	23,950	$	0


			Gross		Gross					Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Fair Value
	Amortized		Unrealized		Unrealized		Fair
	Cost		Gains		Losses		Value
March 31, 2020
December 31, 2019									December 31, 2019
Commercial paper	$	5,983	$	—	$	—	$	5,983	Commercial paper	$	11,940	$	0	$	0	$	11,940
Corporate bonds		11,997		—		(4)		11,993	Corporate bonds	11,990		20		0		12,010
U.S. Treasuries									U.S. Treasuries	13,484		5		0		13,489
	$	17,980	$	—	$	(4)	$	17,976		$	37,414	$	25	$	0	$	37,439