You should read the following discussion and analysis of our financial condition and results of operations together with our consolidated financial statements and related notes appearing elsewhere in this Quarterly Report on Form 10-Q and our Annual Report on Form 10-K for the year ended December 31, 2020, filed with the Securities and Exchange Commission, or SEC, on March 18, 2021 (the "2020 Form 10-K"). Some of the information contained in this discussion and analysis or set forth elsewhere in this Quarterly Report on Form 10-Q, including information with respect to our plans and strategy for our business and related financing, includes forward-looking statements that involve risks and uncertainties. As a result of many factors, including those factors set forth in the "Risk Factors" section elsewhere in this Quarterly Report on Form 10-Q and our 2020 Form 10-K, our actual results could differ materially from the results described in or implied by the forward-looking statements contained in the following discussion and analysis.

Overview

We are a clinical-stage biotechnology company developing cell therapies for patients in multiple therapeutic areas, including cancer, infectious diseases and other serious conditions. We use our proprietary technology, Cell Squeeze®, to physically squeeze cells through a microfluidic chip, temporarily opening the cell membrane and enabling biologic material of interest, or cargo, to diffuse into the cell. This technology allows us to create a broad pipeline of product candidates for different diseases. We believe our Cell Squeeze technology has the potential to create well-tolerated cell therapies that can provide therapeutic benefit for patients. Our potential differentiation includes accelerated timelines with production time under 24 hours, compared to four to six weeks for other existing cell therapies, improved patient experience by eliminating the need for pre-conditioning or lengthy hospital stays, and broadened therapeutic impact. Our goal is to use the Cell Squeeze approach to establish a new paradigm for cell therapies.

We are currently using Cell Squeeze to create multiple cell therapy platforms focused on directing specific immune responses. Our most advanced platform in development, SQZTM Antigen Presenting Cells, or SQZ APCs, is currently in a Phase 1 trial Human Papillomavirus positive, or HPV+, tumors. We presented initial results from the first three cohorts of this ongoing Phase 1 clinical trial of SQZ-PBMC-HPV at the 2021 American Society of Clinical Oncology annual meeting in June 2021. In these cohorts, the investigational cell therapy was observed to be well-tolerated and to stimulate immune responses in certain patients with advanced or metastatic HPV16+ tumors. The trial also demonstrated that our clinical stage manufacturing process of our autologous cell therapy was fast and reliable with production times consistently under 24 hours. Data from the fourth and highest monotherapy dose cohort of this trial will be presented in an oral presentation at the European Society for Medical Oncology Immuno-Oncology Congress in December 2021. As recommended by the independent Data and Safety Monitoring Board, the trial will now advance to the combination stage with checkpoint inhibitors. We have also been developing a next generation SQZ APC platform, enhanced APCs, or eAPCs, that use mRNA as the cargo, which we believe could enhance the functionality of the SQZ APCs to activate CD8 T cells and would be agnostic to patient HLA type. Our additional platforms currently in development are SQZ Activating Antigen Carriers, or SQZ AACs, also entering a Phase 1 trial in HPV+ tumors, and SQZ Tolerizing Antigen Carriers, or SQZ TACs. We have selected Celiac disease as the first autoimmune indication for the SQZ TAC platform with an IND submission targeted for the third quarter of 2022. We are leveraging each of these platforms to create differentiated product candidates that have applicability across multiple disease areas and we are also planning to expand certain of our clinical trials geographically to sites outside of the United States, including in Europe and Asia.

Since our inception, we have focused substantially all of our resources on building our Cell Squeeze technology, establishing and protecting our intellectual property portfolio, conducting research and development activities, developing our manufacturing process and manufacturing product candidate materials, preparing for and initiating clinical trials of our product candidates, organizing and staffing our company, business planning, raising capital and providing general and administrative support for these operations. We do not have any products approved for sale and have not generated any revenue from product sales. Through September 30, 2021, we have funded our operations from sales of common and preferred stock, upfront and milestone payments under our collaboration agreements with Roche and with proceeds from our initial public offering, or IPO, and follow-on public offering of common stock, or the Follow-on Offering. In November 2020, we completed our IPO pursuant to which we issued and sold 5,073,529 shares of common stock, inclusive of 661,764 shares sold by us pursuant to the full exercise of the underwriters' option to purchase additional shares. We received aggregate net proceeds of approximately $75.5 million from the IPO, after deducting underwriting discounts and commissions, but before deducting offering costs payable by us, which were $2.6 million. In February 2021, we completed the Follow-on Offering pursuant to which we issued and sold 3,000,000 shares of common stock. We received aggregate net proceeds of approximately $56.4 million in the Follow-on Offering, after deducting underwriting discounts and commissions, but before deducting offering costs payable by us, which were approximately $0.8 million.

Since our inception, we have incurred significant operating losses. Our ability to generate any product revenue or product revenue sufficient to achieve profitability will depend on the successful development and eventual commercialization of one or more of our product candidates. We reported a net loss of $56.9 million for the nine months ended September 30, 2021. As of September 30, 2021, we had an accumulated deficit of $183.7 million. We expect to continue to incur significant expenses and increasing operating losses for at least the next several years. We expect that our expenses and capital requirements will increase substantially in connection with our ongoing activities, particularly if and as we:



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?
conduct clinical trials for our product candidates, including our ongoing Phase
1 clinical trial of SQZ-PBMC-HPV and SQZ-AAC-HPV;
?
further develop our Cell Squeeze technology;
?
continue to develop additional product candidates;
?
maintain, expand and protect our intellectual property portfolio;
?
hire additional clinical, scientific manufacturing and commercial personnel;
?
expand external and/or establish internal commercial manufacturing sources and
secure supply chain capacity sufficient to provide commercial quantities of any
product candidates for which we may obtain regulatory approval;
?
acquire or in-license other product candidates and technologies;
?
seek regulatory approvals for any product candidates that successfully complete
clinical trials;
?
establish a sales, marketing and distribution infrastructure to commercialize
any products for which we may obtain regulatory approval; and
?
add operational, financial and management information systems and personnel to
support our product development, clinical execution and planned future
commercialization efforts, as well as to continue to support our status as a
public company.

We will not generate revenue from product sales unless and until we successfully complete clinical development and obtain regulatory approval for our product candidates. If we obtain regulatory approval for any of our product candidates, we expect to incur significant expenses related to developing our commercialization capability to support product sales, marketing, and distribution.

As a result, we will need substantial additional funding to support our continuing operations and pursue our growth strategy. Until such time as we can generate significant revenue from product sales, if ever, we expect to finance our operations through a combination of equity offerings, debt financings, collaborations, strategic alliances and marketing, distribution or licensing arrangements. We may be unable to raise additional funds or enter into such other agreements or arrangements when needed on favorable terms, or at all. If we fail to raise capital or enter into such agreements as, and when, needed, we would have to significantly delay, scale back or discontinue the development and commercialization of one or more of our product candidates.

Because of the numerous risks and uncertainties associated with cell therapy product development, we are unable to accurately predict the timing or amount of increased expenses or when, or if, we will be able to achieve or maintain profitability. Even if we are able to generate product sales, we may not become profitable. If we fail to become profitable or are unable to sustain profitability on a continuing basis, then we may be unable to continue our operations at planned levels and be forced to reduce or terminate our operations.

We believe that our existing cash and cash equivalents will enable us to fund our operating expenses and capital expenditure requirements through the first half of 2023. See "-Liquidity and Capital Resources."

Impact of the COVID-19 Coronavirus

In December 2019, a novel strain of coronavirus, which causes the disease known as COVID-19, was reported to have surfaced in Wuhan, China. Since then, COVID-19 coronavirus has spread globally. In March 2020, the World Health Organization declared the COVID-19 outbreak a pandemic and the U.S. government-imposed travel restrictions on travel between the United States, Europe and certain other countries. The outbreak and government measures taken in response have had a significant impact, both direct and indirect, on hospitals, businesses and commerce, as worker shortages have occurred, supply chains have been disrupted, and facilities and production have been suspended. The future progression of the pandemic and its effects on our business and operations are uncertain.

The COVID-19 pandemic has impacted and may continue to impact personnel at third-party manufacturing facilities or the availability or cost of materials, which would disrupt our supply chain. It also has affected and may continue to affect our ability to enroll patients in and timely complete our ongoing Phase 1 clinical trials of SQZ-PBMC-HPV and SQZ-AAC-HPV and delay the initiation of future clinical trials, disrupt regulatory activities or have other adverse effects on our business and operations. For example, we have experienced delays in receiving supplies of raw materials for our preclinical activities due to the impact of COVID-19 on our suppliers' ability to timely manufacture these materials, and we have experienced an increase in the transportation cost of our product candidates due to the decreased availability of commercial flights. In addition, we have experienced delays in opening clinical trial sites and sites that are open may also have challenges enrolling patients due to the COVID-19 pandemic. Further, staff shortages, including staff that are required to conduct certain testing, such as biopsies, at the Company's clinical sites or at third-party vendors have resulted in delays in site initiations and in such tests not being properly or timely performed or being delayed. In response to the public health directives and to help reduce the risk to our employees, we took precautionary measures, including implementing work-from-home policies for our administrative employees and staggered work times for our lab employees. We plan to continue these measures and are assessing when and how to resume normal operations. The effects of the public health directives and our work-from-home policies may negatively



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impact productivity, disrupt our business and delay our clinical programs and timelines and future clinical trials, the magnitude of which will depend, in part, on the length and severity of the restrictions and other limitations on our ability to conduct our business in the ordinary course. These and similar, and perhaps more severe, disruptions in our operations could negatively impact our business, results of operations and financial condition, including our ability to obtain financing.

The pandemic has already caused significant disruptions in the financial markets, and may continue to cause such disruptions, which could impact our ability to raise additional funds to support our operations. Moreover, the pandemic has significantly impacted economies worldwide and could result in adverse effects on our business and operations. We are monitoring the potential impact of the COVID-19 pandemic on our business and financial statements. To date, we have not incurred impairment losses in the carrying values of our assets as a result of the pandemic and we are not aware of any specific related event or circumstance that would require us to revise our estimates reflected in our interim condensed consolidated financial statements. We cannot be certain what the overall impact of the COVID-19 pandemic will be on our business and people. The extent to which the COVID-19 pandemic will directly or indirectly impact our business, results of operations, financial condition, and liquidity, including planned and future clinical trials and research and development costs, will depend on future developments that are highly uncertain, including as a result of new information that may emerge concerning COVID-19, the actions taken to contain or treat it, and the duration and intensity of the related effects.

Components of Our Results of Operations

Revenue

To date, we have not generated any revenue from product sales and do not expect to do so for the next several years. All of our revenue to date has been derived from three collaboration agreements with Roche, which we entered into in 2015, 2017 and 2018, and, to a lesser extent, from government grants.

If our development efforts for our product candidates are successful and result in regulatory approval, or in license or additional collaboration agreements with third parties, we may generate revenue in the future from product sales, payments from additional collaboration or license agreements that we may enter into with third parties, or any combination thereof. We expect that our revenue for the next several years will be derived primarily from our collaboration agreements with Roche as well as any additional collaborations that we may enter into in the future. We cannot provide assurance as to the timing of future milestone or royalty payments or that we will receive any of these payments at all.

Collaboration Revenue

2017 License and Collaboration Agreement with Roche

In April 2017, we entered into a license and collaboration agreement with Roche, or the 2017 Roche Agreement, to allow Roche to use our Cell Squeeze technology to enable gene editing of immune cells to discover new targets in cancer immunotherapy. The 2017 Roche Agreement includes several licenses granted by Roche to us and by us to Roche in order to conduct a specified research program in accordance with a specified research plan.

Under the agreement, we received an upfront payment of $5.0 million as a technology access fee and are entitled to (i) payments of up to $1.0 million as reimbursement for our research costs; (ii) milestone payments of up to $7.0 million upon the achievement of specified development milestones; and (iii) annual maintenance fees ranging from $0.5 million to $0.9 million for each year following the fifth anniversary of the effective date, subject to specified prepayment discounts.

We assessed our accounting for the 2017 Roche Agreement under Accounting Standards Codification, or ASC, 606, Revenue from Contracts with Customers, or ASC 606, and identified the following promises under the agreement: (i) a non-exclusive license granted to Roche to perform research related to and use our Cell Squeeze technology for gene editing of immune cells; (ii) specified research and development services related to gene editing of immune cells through the research term; (iii) manufacturing activities to support the specified research plan; and (iv) participation on a joint research committee, or JRC. We concluded at the outset of the 2017 Roche Agreement that the first three promises should be combined into a single performance obligation and that the JRC participation had an immaterial impact on the accounting model.

We received the upfront payment of $5.0 million in April 2017 upon execution of the 2017 Roche Agreement. We also received the payments of $0.5 million in each of 2017 and 2018 related to our reimbursable research costs. In addition, during the third quarter of 2018, we received a payment of $2.0 million following the achievement of the first development milestone under the agreement related to Roche's validation of preclinical proof of concept.

We recognize revenue associated with the performance obligation as the research and development services are provided using an input method, based on the cumulative costs incurred compared to the total estimated costs expected to be incurred to satisfy the performance obligation. The amounts received from Roche that have not yet been recognized as revenue are deferred as a contract liability in our



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consolidated balance sheet and will be recognized over the remaining research and development period until the performance obligation is satisfied.

During the three and nine months ended September 30, 2021, the total costs expected to be incurred to satisfy the performance obligation under the 2017 Roche Agreement decreased by $0.1 million and $0.4 million, respectively. During the three and nine months ended September 30, 2020, there were no significant changes in the total estimated costs expected to be incurred to satisfy the performance obligation. We recognized revenue of $0.3 million and $0.1 million, under the 2017 Roche Agreement during the three months ended September 30, 2021 and 2020, respectively. We recognized revenue of $1.0 million and $0.4 million, respectively, during the nine months ended September 30, 2021 and 2020 under this agreement.

As of September 30, 2021, we recorded as a contract liability deferred revenue related to the 2017 Roche Agreement of $0.2 million, all of which was a current liability. As of September 30, 2021, the research and development services related to the performance obligation were expected to be performed over a remaining period of approximately nine months.

2018 License and Collaboration Agreement with Roche

In October 2018, we entered into a license and collaboration agreement with Roche, or the 2018 Roche Agreement, to jointly develop certain products based on mononuclear antigen presenting cells, or APCs, including human papilloma virus, or HPV, using our SQZ APC platform for the treatment of oncology indications. We granted Roche a non-exclusive license to our intellectual property, and Roche granted us a non-exclusive license to its and its affiliates' intellectual property for the purpose of performing research activities. In connection with this agreement, the parties terminated an earlier agreement.

Under the 2018 Roche Agreement, Roche was granted option rights to obtain an exclusive license to develop APC products or products derived from the collaboration programs on a product-by-product basis and to develop a Tumor Cell Lysate, or TCL, product. For each of the APC products and TCL product, once Roche exercises its option and pays a specified incremental amount, Roche will receive worldwide, exclusive commercialization rights for the licensed products. Through September 30, 2021, Roche had not exercised any of its options under the 2018 Roche Agreement.

Under the 2018 Roche Agreement, we received an upfront payment of $45.0 million and are eligible to receive (i) reimbursement of a mid-double-digit percentage of our development costs; (ii) aggregate milestone payments on a product-by-product basis of up to $1.6 billion upon the achievement of specified milestones, consisting of up to $217.0 million of development milestone payments, up to $240.0 million of regulatory milestone payments and up to $1.2 billion of sales milestone payments; and (iii) tiered royalties on annual net sales of APC and TCL products licensed under the agreement at specified rates ranging from a mid-single-digit percentage to a percentage in the mid-twenties. We received the upfront payment of $45.0 million in October 2018 upon execution of the agreement. In addition, during the second quarter of 2019, we received a payment of $10.0 million following the achievement of the first development milestone under the 2018 Roche Agreement related to submission by us of preclinical data to the U.S. Food and Drug Administration, or FDA, and during the first quarter of 2020, we received a payment of $20.0 million following the achievement of the second development milestone under the 2018 Roche Agreement related to first-patient dosing in a Phase 1 clinical trial.

We identified three performance obligations at the outset of the 2018 Roche Agreement: (1) the license to our intellectual property, the research and development activities related to HPV through Phase 1 clinical trials under a specified research plan, and the manufacturing of our SQZ APC platform and equipment in order to support the HPV research plan (the "first performance obligation"); (2) the license to our intellectual property and the research and development activities on next-generation APCs (the "second performance obligation"); and (3) the license to our intellectual property and the research and development activities on TCL (the "third performance obligation").

In addition, we determined that the upfront payment of $45.0 million as well as the reimbursable costs of $10.8 million estimated by us constituted the entirety of the consideration to be included in the transaction price. This transaction price of $55.8 million was initially allocated to the three performance obligations based on the relative standalone selling price of each obligation. The potential milestone payments that we may be eligible to receive were excluded from the transaction price at the outset of the arrangement. We reevaluate the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and, if necessary, we will adjust our estimate of the transaction price.

During the second quarter of 2019, we received a payment of $10.0 million following the achievement of the first development milestone under the 2018 Roche Agreement related to submission by us of preclinical data to the FDA. During the first quarter of 2020, we received a payment of $20.0 million following the achievement of the second development milestone under the 2018 Roche Agreement related to first-patient dosing in a Phase 1 clinical trial. These milestones were added to the transaction price in the period that it was "most likely" and that it was probable that a significant reversal in the amount of cumulative revenue recognized would not occur.



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We separately recognize revenue associated with each of the three performance obligations as the research, development and manufacturing services are provided using an input method, based on the cumulative costs incurred compared to the total estimated costs expected to be incurred to satisfy each performance obligation. The amounts received from Roche that have not yet been recognized as revenue are deferred as a contract liability in our consolidated balance sheet and will be recognized over the remaining research and development period until each performance obligation is satisfied.

During the fourth quarter of 2019, we evaluated our overall program priorities and determined that we would continue to focus our resources on progressing the specified APC programs related to the 2018 Roche Agreement as well as our SQZ AAC and SQZ TAC platforms. As a result of its continuing focus on these specific programs, we reduced the level of priority of the TCL research activities under the 2018 Roche Agreement and expect to perform such TCL research activities over a longer time period than as originally expected under the specified research plan of the agreement. Since the fourth quarter of 2019, we have classified $9.2 million as non-current deferred revenue, which will remain unrecognized as revenue until TCL research activities resume or the 2018 Roche Agreement is modified by us and Roche.

During the three and nine months ended September 30, 2021, the estimated costs expected to be incurred to satisfy the performance obligations under the 2018 Roche Agreement increased by $0.4 million. During the three and nine months ended September, 30, 2020, there were no significant changes in the total estimated costs expected to be incurred to satisfy the performance obligations under the 2018 Roche Agreement. We recognized revenue of $4.5 million and $6.0 million during the three months ended September 30, 2021 and 2020, respectively, under this agreement. We recognized revenue of $13.6 million and $18.1 million during the nine months ended September 30, 2021 and 2020, respectively, under the 2018 Roche Agreement. As of September 30, 2021, we recorded as a contract liability deferred revenue related to the 2018 Roche Agreement of $30.4 million, of which $21.2 million was a current liability. As of September 30, 2021, the research and development services related to the performance obligations were expected to be performed over remaining periods ranging from three to nine months.

As of September 30, 2021, the expected remaining period of performance of the Company's research and development services related to the third performance obligation was not determinable, and it will not become determinable until TCL research activities resume or the 2018 Roche Agreement is modified by the Company and Roche.

Operating Expenses

Research and Development Expenses

Research and development expenses consist primarily of costs incurred for our research activities, including development of our product candidates and costs incurred under our collaboration arrangements with Roche, which include:



?
employee-related expenses, including salaries, related benefits and stock-based
compensation expense for employees engaged in research and development
functions;
?
expenses incurred in connection with the preclinical and clinical development of
our product candidates and research programs, including under agreements with
third parties, such as consultants, contractors and contract research
organizations, or CROs;
?
the costs of developing and scaling our manufacturing process and of
manufacturing our product candidates for use in our preclinical studies and
clinical trials, including the costs under agreements with third parties, such
as consultants, contractors and contract manufacturing organizations, or CMOs;
?
laboratory and consumable materials and research materials;
?
facilities, depreciation and other expenses, which include direct and allocated
expenses for rent and utilities; and
?
payments made under third-party licensing agreements.

We expense research and development costs as incurred. Nonrefundable advance payments that we make for goods or services to be received in the future for use in research and development activities are recorded as prepaid expenses. The prepaid amounts are expensed as the related goods are delivered or the services are performed, or when it is no longer expected that the goods will be delivered or the services rendered. Upfront payments under license agreements are expensed upon receipt of the license, and annual maintenance fees under license agreements are expensed in the period in which they are incurred. Milestone payments under license agreements are accrued, with a corresponding expense being recognized, in the period in which the milestone is determined to be probable of achievement and the related amount is reasonably estimable.

Our direct research and development expenses are tracked on a program-by-program basis and consist of external costs and fees paid to consultants, contractors, CMOs and CROs in connection with our preclinical and clinical development and manufacturing activities. Such program costs also include the external costs of laboratory and consumable materials and costs of raw materials that are directly attributable to and incurred for any single program. We do not allocate employee costs, costs associated with our platform development



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and discovery efforts, payments made under third-party licensing agreements, costs of laboratory supplies and consumable materials that are not directly attributable to any single program, and facilities expenses, including rent, depreciation and other indirect costs, to specific product development programs because these costs are deployed across multiple programs and our platform technology and, as such, are not separately classified.

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. We expect that our research and development expenses will increase substantially in connection with our planned preclinical and clinical development activities in the near term and in the future, particularly should Roche determine not to exercise its options and we decide to continue clinical development of a product candidate. At this time, we cannot accurately estimate or know the nature, timing and costs of the efforts that will be necessary to complete the preclinical and clinical development of any of our product candidates. The successful development of our product candidates is highly uncertain. This is due to the numerous risks and uncertainties associated with product development, including the following:



?
the timing and progress of preclinical and clinical development activities,
including geographic expansion of our clinical sites into Europe and Asia;
?
the number and scope of preclinical and clinical programs we decide to pursue;
?
raising additional funds necessary to complete preclinical and clinical
development of our product candidates;
?
the progress of the development efforts of parties with whom we have entered, or
may enter, into collaboration arrangements;
?
our ability to maintain our current research and development programs and to
establish new ones;
?
our ability to establish new licensing or collaboration arrangements;
?
the successful initiation and completion of clinical trials with safety,
tolerability and efficacy profiles that are satisfactory to the FDA or any
comparable foreign regulatory authority;
?
the receipt and related terms of regulatory approvals from applicable regulatory
authorities;
?
the availability of specialty raw materials for use in production of our product
candidates;
?
our ability to consistently manufacture our product candidates for use in
clinical trials;
?
our ability to establish and operate a manufacturing facility, or secure
manufacturing supply through relationships with third parties;
?
our ability to obtain and maintain patents, trade secret protection and
regulatory exclusivity, both in the United States and internationally; and
?
our ability to protect our rights in our intellectual property portfolio.

A change in the outcome of any of these variables with respect to the development of any of our product candidates could significantly change the costs and timing associated with the development of that product candidate. In addition, we may never succeed in obtaining regulatory approval for any of our product candidates.

General and Administrative Expenses

General and administrative expenses consist primarily of salaries and related costs, including stock-based compensation, for personnel in executive, finance and administrative functions. General and administrative expenses also include direct and allocated facility-related costs as well as professional fees for legal, patent, consulting, investor and public relations, accounting, and audit services. We anticipate that our general and administrative expenses will increase in the future as we increase our headcount to support our continued research activities and development of our product candidates. We also anticipate that we will incur increased accounting, audit, legal, regulatory, compliance and director and officer insurance costs as well as investor and public relations expenses associated with operating as a public company.

Other Income (Expense)

Interest Income

Interest income consists of interest earned on our cash equivalents and marketable securities balances.

Other Income (Expense), Net

Other income (expense), net consists of miscellaneous income and expense unrelated to our core operations.



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Income Taxes

Since our inception, we have not recorded any income tax benefits for the net losses we have incurred in each year or for our earned research and development tax credits, as we believe, based upon the weight of available evidence, that it is more likely than not that all of our net operating loss carryforwards and tax credit carryforwards will not be realized.

On March 27, 2020, the Coronavirus Aid, Relief and Economic Security Act, or the CARES Act, was passed by the U.S. Congress and signed into United States law. The CARES Act, among other things, includes certain provisions for individuals and corporations (including a suspension on the application of the 80% limitation described above for taxable years beginning prior to January 1, 2021), and technical amendments for qualified improvement property, or QIP. While we accelerated tax depreciation expenses due to the technical amendments made by the CARES Act to QIP, this and other CARES Act benefits did not materially impact our income tax provisions in the periods presented.

Results of Operations

Comparison of the Three Months Ended September 30, 2021 and 2020

The following table summarizes our results of operations for the three months ended September 30, 2021 and 2020:





                                   THREE MONTHS ENDED
                                     SEPTEMBER 30,
                                    2021             2020        CHANGE
                                            (in thousands)
Collaboration revenue                    $4,755       $6,121     $(1,366)
Operating expenses:
Research and development                 20,520       13,910        6,610
General and administrative                6,691        4,612        2,079
Total operating expenses                 27,211       18,522        8,689
Loss from operations                   (22,456)     (12,401)     (10,055)
Other income (expense):
Interest income                               8           56         (48)
Other income (expense), net                 (2)          (6)            4
Total other income, net                       6           50         (44)
Net loss                              $(22,450)    $(12,351)    $(10,099)




Revenue

Collaboration revenue decreased by $1.4 million to $4.8 million for the three months ended September 30, 2021, compared to $6.1 million for the three months ended September 30, 2020. The decrease in revenue was primarily due to the following:



?

a decrease of $1.5 million to $4.5 million from $6.0 million in revenue recognized under the 2018 Roche Agreement due to a change in estimate (made as of December 2020) of the expected performance period of one of the performance obligations under the 2018 Roche Agreement, resulting in lower revenues being recognized in the third quarter of 2021.

Research and Development Expenses





                                                   THREE MONTHS ENDED
                                                      SEPTEMBER 30,
                                                   2021            2020           CHANGE
                                                              (in thousands)
Direct research and development expenses by
program:
SQZ-PBMC-HPV                                        $4,187           $3,908           $279
SQZ-AAC-HPV                                            895            2,893        (1,998)
eAPC                                                 6,393              399          5,994
Other programs                                       1,369              864            505
Unallocated research and development
expenses:
Personnel related (including stock-based
compensation)                                        5,317            3,792          1,525
Facility related                                     1,251            1,204             47
Laboratory and consumable materials                    389              218            171
Platform-related external services and other           719              632             87
Total research and development expenses            $20,520          $13,910         $6,610

Research and development expenses increased by $6.6 million to $20.5 million for the three months ended September 30, 2021, from $13.9 million for the three months ended September 30, 2021. The net increase was primarily due to the following:





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?
SQZ-PBMC-HPV program costs increased by $0.3 million primarily as a result of an
increase in clinical batch manufacturing and patient costs.
?
SQZ-AAC-HPV costs decreased by $2.0 million primarily as a result of a decrease
in start up manufacturing costs which were primarily incurred in 2020.
?
eAPC costs increased by $6.0 million due to higher manufacturing and materials
costs incurred.
?
Other program costs increased by $0.5 million due to spending on our infectious
disease program, as well as other manufacturing costs.
?
The increase in personnel-related costs of $1.5 million was primarily due to a
$1.1 million increase in stock-based compensation expense and a $0.4 million
increase in salary and benefit costs as a result of increased headcount in our
research and development function.
?
Laboratory and consumable materials expenses increased by $0.2 million as a
result of expected fluctuations from period to period based on the timing of our
purchases made.
?
Platform-related external services and other costs increased by $0.1 million as
a result of higher consulting, equipment and information technology costs.

General and Administrative Expenses





                                                 THREE MONTHS ENDED
                                                   SEPTEMBER 30,
                                                2021           2020         CHANGE
                                                          (in thousands)
Personnel related (including stock-based
compensation)                                     $3,207         $2,026        $1,181
Professional, consultant and patent
related costs                                      1,709          1,673            36
Facility related and other                         1,775            913           862

Total general and administrative expenses $6,691 $4,612 $2,079

General and administrative expenses increased by $2.1 million during the three months ended September 30, 2021 to $6.7 million, compared to $4.6 million for the three months ended September 30, 2020. The increase was primarily due to:





?

an increase of $1.2 million in personnel-related costs due to a $0.9 million increase in stock-based compensation expense and a $0.3 million increase in salary and benefit costs as a result of increased headcount.

Comparison of the Nine Months Ended September 30, 2021 and 2020

The following table summarizes our results of operations for the nine months ended September 30, 2021 and 2020:





                                 NINE MONTHS ENDED
                                   SEPTEMBER 30,
                                2021          2020         CHANGE
                                         (in thousands)
Revenue:

Collaboration revenue $ 14,748 $ 18,511 $ (3,763 ) Operating expenses: Research and development 52,942 37,815 15,127 General and administrative 18,744 14,139 4,605 Total operating expenses 71,686 51,954 19,732 Loss from operations

            (56,938 )     (33,443 )     (23,495 )
Other income (expense):
Interest income                      28           533          (505 )
Other income (expense), net          (9 )         (10 )           1
Total other income, net              19           523          (504 )
Net loss                      $ (56,919 )   $ (32,920 )   $ (23,999 )




Revenue

Collaboration revenue decreased by $3.8 million to $14.7 million for the nine months ended September 30, 2021, compared to $18.5 million for the nine months ended September 30, 2020. The decrease in revenue was primarily due to the following:



?

a decrease of $4.5 million to $13.6 million from $18.1 million in revenue recognized under the 2018 Roche Agreement due to a change in estimate (made as of December 2020) of the expected performance period of one of the performance obligations under the 2018 Roche Agreement, resulting in lower revenues being recognized in the nine months ended September 30, 2021.



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The above decrease was partially offset by:



?

an increase of $0.6 million in revenue recognized under the 2017 Roche Agreement during the nine months ended September 30, 2021, compared to the nine months ended September 30, 2020. The increase in revenue was due to a decrease in remaining expected costs required to complete the performance obligations under the 2017 Roche Agreement.

Research and Development Expenses



                                                  NINE MONTHS ENDED
                                                    SEPTEMBER 30,
                                                 2021            2020          CHANGE
                                                            (in thousands)
Direct research and development expenses by
program:
SQZ-PBMC-HPV                                  $    11,314     $   11,501     $      (187 )
SQZ-AAC-HPV                                         3,005          5,322          (2,317 )
eAPC                                               11,607          1,365          10,242
Other programs                                      5,870          2,357           3,513
Unallocated research and development
expenses:
Personnel related (including stock-based
compensation)                                      13,991         10,530           3,461
Facility related                                    3,816          3,806              10
Laboratory and consumable materials                   985            748             237
Platform-related external services and
other                                               2,354          2,186             168

Total research and development expenses $ 52,942 $ 37,815 $ 15,127

Research and development expenses increased by $15.1 million to $52.9 million for the nine months ended September 30, 2021, compared to $37.8 million for the nine months ended September 30, 2020. The net increase was primarily due to the following:





?
SQZ-PBMC-HPV costs decreased by $0.2 million primarily as a result of our
transferring certain externally performed services in-house.
?
SQZ-AAC-HPV costs decreased by $2.3 million primarily as a result of the timing
of materials and manufacturing costs.
?
eAPC costs increased by $10.2 million due to higher manufacturing costs
incurred.
?
Other program costs increased by $3.5 million due to spending on our infectious
disease program and expenses incurred on developing a point-of-care solution to
manufacture our product candidates.
?
an increase of $3.5 million in personnel-related costs was primarily due to a
$1.6 million increase in salary and benefit costs as a result of increased
headcount and salary costs in our research and development function, and a $1.9
million increase in stock-based compensation expense.
?
Laboratory and consumable materials costs increased by $0.2 million as a result
of expected fluctuations from period to period based on the timing of our
purchases made.
?
Platform-related external services increased by $0.2 million due to an increase
in professional services costs.



General and Administrative Expenses





                                                  NINE MONTHS ENDED
                                                    SEPTEMBER 30,
                                                 2021            2020           CHANGE
                                                            (in thousands)
Personnel related (including stock-based
compensation)                                $      9,141     $     6,195     $     2,946
Professional, consultant and patent
related costs                                       4,398           5,417          (1,019 )
Facility related and other                          5,205           2,527           2,678

Total general and administrative expenses $ 18,744 $ 14,139 $ 4,605

General and administrative expenses increased by $4.6 million for the nine months ended September 30, 2021 to $18.7 million, compared to $14.1 million for the nine months ended September 30, 2020. The increase was primarily due to the following:





?
an increase of $2.9 million in personnel-related costs due to a $2.1 million
increase in stock-based compensation expense and a $0.8 million increase in
salary and benefit costs as a result of increased headcount.
?
a decrease of $1.0 million in professional, consultant and patent related costs
as the costs incurred in the prior year period were primarily incurred to
support our preparation to become a public company.
?
an increase of $2.7 million in facility-related and other costs primarily due to
an increase in insurance expense as a public company for the nine months ended
September 30, 2021.

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Interest Income

Interest income for the nine months ended September 30, 2021, was less than $0.1 million as compared to $0.5 million for the nine months ended September 30, 2020. The decrease in interest income was due to the decrease in average interest rates during the respective periods.

Liquidity and Capital Resources

Since our inception, we have incurred significant operating losses. We have not yet commercialized any of our product candidates and we do not expect to generate revenue from sales of any product candidates for the next several years, if at all. Through September 30, 2021, we have funded our operations from the sales of our common and preferred stock, upfront and milestone payments under our collaboration agreements with Roche, and with proceeds from our IPO and Follow-on Offering. In November 2020, we completed our IPO pursuant to which we received aggregate net proceeds of approximately $72.9 million from the sale of common stock. In February 2021, we completed the Follow-on Offering pursuant to which we received aggregate net proceeds of approximately $55.6 million from the sale of common stock. As of September 30, 2021, we had cash and cash equivalents of $164.3 million.

Cash Flows



The following table summarizes our sources and uses of cash for each of the
periods presented:



                                                                NINE MONTHS ENDED
                                                                  SEPTEMBER 30,
                                                               2021          2020
                                                                 (in thousands)
Net cash used in operating activities                        $ (61,117 )   $ (23,912 )
Net cash (used in) provided by investing activities               (613 )      49,946
Net cash provided by financing activities                       55,627        41,757

Net increase in cash, cash equivalents and restricted cash $ (6,103 ) $ 67,791






Operating Activities

During the nine months ended September 30, 2021, operating activities used $61.1 million of cash, primarily resulting from our net loss of $56.9 million and changes in our operating assets and liabilities of $18.7 million, partially offset by net non-cash charges of $14.5 million. Net cash used by changes in our operating assets and liabilities for the nine months ended September 30, 2021 consisted primarily of a $14.5 million decrease in deferred revenue, a $6.8 million decrease in operating lease liabilities, a $1.4 million decrease in accrued expenses, all of which were partially offset by a $2.7 million decrease in prepaid expenses and other current assets and a $1.9 million decrease in accounts receivable. The decrease in deferred revenue during the nine months ended September 30, 2021 was due to the revenue we recognized in that same period under the 2018 Roche Agreement.

During the nine months ended September 30, 2020, operating activities used $23.9 million of cash, primarily resulting from our net loss of $32.9 million and changes in our operating assets and liabilities of $1.5 million, partially offset by net non-cash charges of $10.5 million. Net cash used by changes in our operating assets and liabilities for the nine months ended September 30, 2020 consisted primarily of a $6.6 million decrease in operating lease liabilities, a $2.1 million decrease in accounts payable and accrued expenses and a $0.2 million increase in prepaid expenses and other current assets, all as partially offset by a $0.3 million decrease in other liabilities and a $7.2 million increase in deferred revenue. The increase in deferred revenue during the nine months ended September 30, 2020 was due to our receipt of a $20.0 million milestone payment, partially offset by the related revenue we recognized in that same period, under the 2018 Roche Agreement.

In all periods presented, other changes in prepaid expenses and other current assets, accounts receivable, accounts payable, accrued expenses and other liabilities not described above were generally due to growth in our business, the advancement of our research programs and the timing of vendor invoicing and payments. In all periods presented, decreases in operating lease liabilities were primarily due to our recurring payments made under recorded operating lease liabilities, including those arising from embedded leases.

Investing Activities

During the nine months ended September 30, 2021, net cash used in investing activities was $0.6 million, consisting of purchases of property and equipment.

During the nine months ended September 30, 2020, net cash provided by investing activities was $49.9 million, consisting of maturities of marketable securities of $51.0 million, partially offset by purchases of property and equipment of $1.1 million

The purchases of property and equipment in each period were primarily for equipment purchases and leasehold improvements related to the expansion of our research and development activities and the growth of our business.



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Financing Activities

During the nine months ended September 30, 2021, net cash provided by financing activities was $55.6 million, consisting of net proceeds from the Follow-on Offering in February 2021, of $56.4 million, in addition to proceeds of $1.1 million from stock option exercises during the period, offset by the payment of $1.9 million of IPO and Follow-on Offering costs.

During the nine months ended September 30, 2020, net cash provided by financing activities was $41.8 million, consisting primarily of net proceeds from our issuances of Series D preferred stock, partially offset by $0.3 million of payments of IPO costs and $0.2 million of payments of issuance costs related to Series D preferred stock that we issued and sold in December 2019.

Funding Requirements

We expect that our expenses will increase substantially in connection with our ongoing activities, particularly as we advance the preclinical activities and clinical trials for our product candidates in development. The timing and amount of our operating and capital expenditures will depend largely on:



?
the timing and progress of preclinical and clinical development activities,
including geographic expansion of our clinical sites into Europe and Asia;
?
the commencement, enrollment or results of the planned clinical trials of our
product candidates or any future clinical trials we may conduct, or changes in
the development status of our product candidates;
?
the timing and outcome of regulatory review of our product candidates;
?
our decision to initiate a clinical trial, not to initiate a clinical trial or
to terminate an existing clinical trial as well as Roche's decision whether to
exercise its options;
?
changes in laws or regulations applicable to our product candidates, including
but not limited to clinical trial requirements for approvals;
?
adverse developments concerning our manufacturers;
?
our ability to obtain materials to produce adequate product supply for any
approved product or inability to do so at acceptable prices;
?
our ability to establish collaborations if needed;
?
the costs and timing of future commercialization activities, including product
manufacturing, marketing, sales and distribution, for any of our product
candidates for which we obtain marketing approval;
?
the legal patent costs involved in prosecuting patent applications and enforcing
patent claims and other intellectual property claims;
?
additions or departures of key scientific or management personnel;
?
unanticipated serious safety concerns related to the use of our product
candidates;
?
the terms and timing of any collaboration, license or other arrangement,
including the terms and timing of any milestone payments thereunder; and
?
the severity, duration and impact of the COVID-19 pandemic, which may adversely
impact our business.

We believe that our existing cash and cash equivalents will enable us to fund our operating expenses and capital expenditure requirements through the first half of 2023. We have based this estimate on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we expect.

Until such time, if ever, as we can generate substantial product revenue, we expect to finance our operations through a combination of equity offerings, debt financings, collaborations, strategic alliances and marketing, distribution or licensing arrangements. To the extent that we raise additional capital through the sale of equity or convertible debt securities, a current common stockholder's interest will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of a common stockholder. Debt financing and preferred equity financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making acquisitions or capital expenditures or declaring dividends. If we raise additional funds through collaborations, strategic alliances or marketing, distribution 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 grant licenses on terms that may not be favorable to us. If we are unable to raise additional funds through equity or debt financings or other arrangements when needed, we would be required to delay, scale back or discontinue our research, product development or future commercialization efforts, or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.



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Contractual Obligations and Commitments

There have been no material changes to our contractual obligations from those described in our 2020 Form 10-K. For additional information, see Note 9 to our consolidated financial statements appearing in this Quarterly Report on Form 10-Q.

Critical Accounting Policies and Significant Judgments and Estimates

Our financial statements are prepared in accordance with generally accepted accounting principles in the United States. The preparation of our financial statements and related disclosures requires us to make estimates, assumptions and judgments that affect the reported amount of assets, liabilities, revenue, costs and expenses, and related disclosures. Our critical accounting policies are described under the heading "Management's Discussion and Analysis of Financial Condition and Results of Operations-Critical Accounting Policies and Significant Judgments and Estimates" in our 2020 Form 10-K. If actual results or events differ materially from the estimates, judgments and assumptions used by us in applying these policies, our reported financial condition and results of operations could be materially affected. There have been no significant changes to our critical accounting policies from those described in the 2020 Form 10-K.

Off-Balance Sheet Arrangements

We did not have during the periods presented, and we do not currently have, any off-balance sheet arrangements, as defined in the rules and regulations of the SEC.

Recently Issued Accounting Pronouncements

A description of recently issued accounting pronouncements that may potentially impact our financial position, results of operations or cash flows is disclosed in Note 2 to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

Emerging Growth Company Status

The Jumpstart Our Business Startups Act of 2012 permits an "emerging growth company" such as us to take advantage of an extended transition period to comply with new or revised accounting standards applicable to public companies until those standards would otherwise apply to private companies. We have elected not to "opt out" of such extended transition period, which means that when a standard is issued or revised and it has different application dates for public or private companies, we will adopt the new or revised standard at the time private companies adopt the new or revised standard and will do so until such time that we either (i) irrevocably elect to "opt out" of such extended transition period or (ii) no longer qualify as an emerging growth company. We may choose to early adopt any new or revised accounting standards whenever such early adoption is permitted for private companies.

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