The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our consolidated financial statements and related notes included elsewhere in this Annual Report on Form 10-K. This discussion and analysis and other parts of this Annual Report on Form 10-K contain forward-looking statements based upon current beliefs, plans and expectations that involve risks, uncertainties and assumptions, such as statements regarding our plans, objectives, expectations, intentions and projections. Our actual results and the timing of selected events could differ materially from those anticipated in these forward-looking statements as a result of several important factors, including without limitation those set forth under "Summary Risk Factors," Part I, Item 1A "Risk Factors" and elsewhere in this Annual Report on Form 10-K. You should carefully read the "Risk Factors" section of this Annual Report on Form 10-K to gain an understanding of the important factors that could cause actual results to differ materially from our forward-looking statements. Please also see the section entitled "Special Note Regarding Forward-Looking Statements." A discussion of the year ended December 31, 2021 compared to the year ended December 31, 2020, as well as a discussion of our 2020 fiscal year, specifically, has been reported previously in our Annual Report on Form 10-K for the year ended December 31, 2021, filed with the SEC on March 24, 2022, under the heading "Management's Discussion and Analysis of Financial Condition and Results of Operations."

Overview

Evelo is a clinical-stage biotechnology company focused on discovering and developing a new class of oral medicines that act on immune cells in the small intestine with systemic effects.

We believe the small intestine has a profound influence on systemic immunity and can resolve inflammation throughout the body. We have discovered that specific single strains of microbes resident in the mucosal lining of the small intestine, and the extracellular vesicles they shed, have the potential to resolve inflammation throughout the body when given orally at pharmacological doses, by physically interacting with immune cells in the small intestine. Engagement in the small intestine can lead to the generation of circulating T cells with regulatory activity that down-regulate multiple inflammatory pathways, including Th1, Th2 and Th17, without suppressing immunity. Our investigational medicines have not been observed to colonize the gut nor modify the microbiome.

This discovery may create the potential for a new type of effective, safe, well tolerated, and convenient medicine for people with many types and stages of inflammatory diseases. Evelo initially is developing EDP1815 as a treatment in psoriasis and atopic dermatitis and EDP2939 in psoriasis. If shown to be effective in inflammatory disease mediated by the Th1, Th2 or Th17 inflammatory pathways, we believe these same investigational medicines have potential utility in additional inflammatory diseases, such as psoriatic and other forms of arthritis, asthma, allergy, and inflammatory bowel disease.

Clinical Programs

EDP1815

EDP1815 is an investigational oral biologic being developed for the treatment of inflammatory diseases. It is a single strain of Prevotella histicola isolated from a human donor and selected for its specific pharmacology. EDP1815 is currently in clinical development for both psoriasis, driven largely by Th17 inflammation, and atopic dermatitis, driven by TH2 inflammation.

Psoriasis

Preparation for registration trials

Following completion of the Phase 2 trial of EDP1815 in psoriasis described below, we are undertaking various activities to prepare for potential registration trials of EDP1815 in psoriasis, advancement into which is funding dependent, including CMC preparations, protocol development and regulatory agency consultation.

We have received feedback from the FDA, EMA and MHRA regarding our proposed registration trial design of EDP1815 in psoriasis, including the primary and secondary endpoints. We also sought feedback and discussed critical components of the CMC for EDP1815 with EMA and MHRA, particularly our proposals regarding product release and stability testing. We reached alignment regarding: use of a primary endpoint of PGA 0/1 with a 2-point improvement; no need for an active comparator in Europe, with placebo control acceptable in the mild-to-moderate population; and CMC plan for release and stability testing panels. We believe the regulatory feedback provides a




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path toward registration trials in psoriasis and we are incorporating the agencies' comments into our Phase 3 trial designs and related preparatory work.

Phase 2 clinical trial

In September 2021, we announced positive data from a Phase 2 trial of EDP1815 in psoriasis. This multicenter, randomized, double-blind, placebo-controlled, dose-ranging Phase 2 trial evaluated three doses of EDP1815 in adult patients with mild and moderate psoriasis. The trial included a treatment phase (Part A) and an off-treatment, follow-up phase (Part B). In Part A of the trial, 249 patients were randomized in a 1:1:1 ratio to one of three parallel cohorts: 1 capsule, 4 capsules or 10 capsules. They were then randomized in a 2:1 ratio to active or placebo prior to the start of dosing. Trial medication was taken once daily for 16 weeks, and all patients were followed for 4 weeks after treatment completion to week 20. PASI scores were assessed by both mean changes from baseline and responder rates. The primary endpoint was the mean percentage change in PASI scores between treatment and placebo at 16 weeks. Secondary endpoints included the proportion of study patients who achieved at least a 50% improvement in PASI from baseline at the week 16 timepoint, and other clinical measures of disease such as PGA, BSA, PGA x BSA, PSI, and DLQI.

The primary endpoint, the difference in mean percentage change in PASI scores from baseline at week 16 between treatment and placebo, was prespecified as a Bayesian analysis. The Bayesian approach provides an estimate of the probability that EDP1815 was superior to placebo. The 16-week primary endpoint gave probabilities that EDP1815 is superior to placebo ranging from 80% to 90% across the prespecified analyses and cohorts.

The responder endpoint analysis evaluated the proportion of patients who achieved a PASI-50 (a meaningful clinical response) or greater reduction in PASI score at week 16. 25% to 32% of patients across the three EDP1815 treated cohorts achieved a PASI-50 or greater reduction at week 16 compared to 12% on placebo. In cohorts 1 and 2, this difference in response rate was statistically significant (p <0.05). Cohort 3 was not statistically significant, but directionally similar (25% vs. 12%). The pooled PASI-50 response across all three EDP1815 cohorts, an exploratory analysis, was 29% vs. 12% for placebo and was also statistically significant with a p-value of 0.027. An increase in the number of capsules of EDP1815 did not lead to a dose response.



                    [[Image Removed: evlo-20221231_g4.jpg]]

*p<0.05.

PASI-50 responses at week 16. Statistically significant p-value (<0.05) for 2 of the 3 individual dose cohorts, and for all 3 cohorts when pooled

Additionally, several patients on EDP1815 achieved a PASI-75 response or better at week 16. For individuals who had a PASI-50 response or better, consistent improvements in patient reported outcomes such as DLQI and PSI were observed.

EDP1815 was observed to be well tolerated in Part A (treatment phase) of the trial. The safety data were comparable to placebo. Adverse events classified as "gastrointestinal" were comparable between active and placebo groups, with no meaningful differences in rates of diarrhea, abdominal pain, nausea, or vomiting. There were no drug related serious adverse events.




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All patients in Part A had the option to enter Part B (extended follow-up phase, off-treatment) of the trial. The objective of Part B was to assess durability of treatment response and incidence of rebound (for example, increase in PASI score to 125% of baseline value or above, or onset of new pustular erythrodermic psoriasis within 3 months) following cessation of dosing. All patients who elected to enroll in Part B were assessed during follow-up visits at weeks 24 and 28. Patients who had achieved a PASI-50 or greater at week 16 were also evaluated at week 40. Patients were not permitted to start other psoriasis treatments or trials during Part B.

In February 2022 we announced data from Part B, which included durable and deeper clinical responses. Eighty-three patients who had received EDP1815 in Part A entered Part B. Thirty of these 83 patients had achieved a PASI-50 or greater reduction at week 16 in Part A. Eighteen of the 30 patients remained at PASI-50 or greater at the end of Part B. Ten of the 30 patients had achieved a PASI-75 or greater at the end of Part A and 5 remained at PASI-75 or greater at the end of Part B. These durable results were achieved without any new psoriasis medication being used during this time. Nineteen of the 83 patients had achieved clear skin (PGA 0) or nearly clear skin (PGA 1) at the end of Part A and of these, 9 remained at PGA 0/1 at the end of Part B.

Of the 30 patients who had reached a PASI-50 at the end of Part A and entered Part B, 10 had already achieved a PASI-75 response at week 16 in Part A. Of the remaining 20 patients, 9 achieved a PASI-75 or greater response during the post-treatment period. These data, combined with the durability data, suggest that longer dosing could lead to further deepening of the responses in some patients.

There were no drug related adverse events in Part B, with the additional finding of no flare or rebound following cessation of dosing (which are seen with some other therapies for psoriasis).

In February 2022, we also announced the results of immunological biomarker analyses from Part A of the Phase 2 trial in psoriasis. We had previously reported reductions in inflammatory cytokines in a Phase 1b trial of EDP1815 in mild and moderate psoriasis, and these data were replicated in the Phase 2 psoriasis trial, with high statistical significance.

Blood samples were taken from 96 patients at baseline and after 16 weeks of dosing with EDP1815 or placebo. The figures below show the changes in pro-inflammatory cytokines interleukin 6 (IL-6), interleukin 8 (IL-8) and tumor necrosis factor (TNF). Each vertical bar represents the fold change up or down from 0 in ex vivo stimulated cytokine production between the baseline and week 16 samples from a patient. Three different stimuli were used on each sample and the results from all three stimuli are presented together in the figures, giving the aggregate N (sample) numbers shown in the figures.

Treatment with EDP1815 led to a statistically significant reduction in the release of cytokines compared to placebo: IL-6 (p=0.0003), IL-8 (p=0.0007), and TNF (p=0.0037). The effect observed for EDP1815 may be clearly seen by the deep tail of reduced cytokine production on the left of the distribution for each cytokine, which was absent in the placebo groups. There was no worsening compared to placebo on the right of the distributions, resulting in the overall significant difference between EDP1815 and placebo.



                    [[Image Removed: evlo-20221231_g5.jpg]]

In addition, skin biopsies of active lesions were taken from a subset of patients in the trial. Six of the patients who received EDP1815 and achieved at least a PASI-50 response from baseline at week 16 had paired biopsies.




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RNAseq analysis of the biopsies showed reductions in transcript levels for psoriasis-relevant cytokines interleukin 23 (IL-23), interleukin 12b (IL-12b), and interleukin 17 (IL-17) in these lesions between baseline and week 16. The box plot below shows the median and interquartile ranges, as well as individual values of the cytokine expression levels in the skin, at baseline and week 16. These data suggest that EDP1815 reduced inflammation in the skin by modulating multiple proinflammatory cytokines.


                    [[Image Removed: evlo-20221231_g6.jpg]]

We believe these data support the biology of the SINTAX and the development of a new potential class of medicine that is designed to act locally in the small intestine to affect inflammation throughout the body. In the Phase 2 trial, there was no observed distribution of EDP1815 outside the gut.

Pediatric Investigation Plan for EDP1815 in Psoriasis

In February 2022, the EMA agreed to our PIP for EDP1815 in psoriasis, in accordance with Regulation (EC) No 1901/2006 of the European Parliament and of the Council. The EMA agreement allows Evelo to include patients 12-17 years old in Phase 3 trials, conduct a single clinical trial in patients 2-5 years old and 6-11 years old after the adult MAA has been submitted, and develop a pediatric formulation suitable for administration to patients 2-11 years old. Furthermore, the EMA confirmed that juvenile toxicity studies are not required for EDP1815 and granted us a waiver from studying EDP1815 in patients less than 2 years old.

Atopic dermatitis

Phase 2 clinical trial

In February 2022, we began dosing patients in a Phase 2 trial of EDP1815 in atopic dermatitis. The primary objective of this multicenter, randomized, double-blind, placebo-controlled multiple cohort trial is to evaluate the efficacy and safety of EDP1815 in the treatment of atopic dermatitis when dosed for 16 weeks, compared to placebo. The trial is enrolling patients with mild, moderate, and severe atopic dermatitis and each of the four cohorts is investigating a different aspect of the potential of EDP1815 in the treatment of atopic dermatitis.

The primary endpoint for the trial is the proportion of patients who achieve an outcome of a 50% improvement from baseline in EASI score at week 16. Secondary endpoints include several physician-reported outcomes, such as IGA and BSA, along with patient-reported outcomes such as DLQI, daily itch using the Pruritus-NRS, and POEM. Patients will be randomized into one of four cohorts. Cohorts 1-3 include approximately 100 patients per cohort randomized in a 3:1 ratio (75 to EDP1815 and 25 to placebo) for a total of approximately 300 patients. Patients in Cohort 4 are randomized in a 2:1 ratio (70 to EDP1815 and 35 to placebo) for a total of approximately 105 patients.

Each cohort in the trial is independently tested for the potential of EDP1815 in the treatment of atopic dermatitis, as well as specific hypotheses with regards to cell concentration, manufacturing process, dosing regimen and site of release. Cohort 1 explored a daily dose of 1.6 x 1011 total cells of EDP1815 or matching placebo administered as two capsules once daily. Patients dosed in this cohort received the same EDP1815 drug product as used in the previously completed Phase 2 psoriasis study which demonstrated an improvement in PASI-50 responses (as defined below). This was intended to allow a relative comparison of the benefit observed in psoriasis patients during the Phase 2 trial with any observed benefit in atopic dermatitis patients. Cohort 2 of the atopic dermatitis trial tested 6.4 x 1011 total cells of EDP1815 or matching placebo administered as two capsules once daily. This higher concentration of EDP1815 drug product was produced using a different manufacturing process, which was intended




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to allow an assessment of the clinical activity of a higher concentration of EDP1815 in a single capsule and of the alternate manufacturing process. Cohort 3 used the same drug product and daily dose as Cohort 2 (or matching placebo), but was administered as one capsule taken twice daily. This cohort was intended to test if there was any additional benefit obtained from a twice a day regimen versus once a day. Patients in Cohort 4 receive EDP1815 (8.0 x 1010 total cells) in a faster release capsule that releases the drug product higher up in the small intestine than the capsule used in the other three cohorts, or matching placebo. The Cohort 4 drug product has been manufactured using the same drug substance manufacturing process as in Cohort 1. Cohort 4 is evaluating if release of EDP1815 higher up in the small intestine provides greater clinical activity, as separate preclinical study data has previously demonstrated that higher release resulted in improved pharmacodynamic effects against inflammation in mice. All patients in Cohort 4 will have the opportunity to join an open-label extension trial once they complete 16 weeks of dosing. Patients in the open-label extension trial will receive EDP1815 for a further 36 weeks.

In February 2023, we announced interim data from our Phase 2 trial of EDP1815 in atopic dermatitis. Cohorts 1, 2 and 3 of the trial failed to meet the primary endpoint, which is the proportion of patients who achieve an outcome of EASI-50 response, compared to placebo at week 16. EASI-50 responses or greater were achieved in 41%, 38% and 32% of patients with mild to moderate disease at week 16, in cohorts 1, 2 and 3 respectively. Patients on placebo had an overall EASI-50 response of 56% and placebo responses varied significantly by geography. We are evaluating the data to understand the very high placebo response rates observed in Cohorts 1-3 of the trial, which occurred with greater prevalence in certain geographic regions. No conclusions regarding the cause of the high placebo response have yet been identified, but analysis is on-going. In all three cohorts, EDP1815 was well-tolerated.

Cohort 4 of the Phase 2 trial of EDP1815 in atopic dermatitis is fully recruited and is testing a faster release capsule, intended to deliver EDP1815 higher up in the small intestine, that may potentially enable greater clinical activity. Data from this cohort of patients is expected in the second quarter of 2023 and will inform our path forward for EDP1815 in patients with atopic dermatitis.

Scintigraphy Studies

We continue to evaluate different formulations of EDP1815 with the goal of providing optimum delivery of the drug substance in the small intestine. We completed a Phase 1 single center clinical trial in healthy human volunteers that assessed the release characteristics of different formulations (capsules and tablets) of EDP1815 by gamma scintigraphy imaging. In March 2022, results from the Phase 1 trial showed that a capsule with an improved release profile was able to deliver EDP1815 higher up in the small intestine. In 17 of the human volunteers studied, 15 (or 88%) showed that EDP1815 released in the jejunum, the upper part of the small intestine. Preclinical data have shown that the higher that EDP1815 is released in the small intestine, the greater the observed effect. We are evaluating this faster release capsule in Cohort 4 of our Phase 2 trial of EDP1815 in atopic dermatitis and in Phase 1/2 trial of EDP2939 in psoriasis.

Other Indications

We intend to evaluate EDP1815 in additional inflammatory disease indications. Potential indications may include psoriatic arthritis, asthma, axial spondylarthritis and rheumatoid arthritis.

EDP2939

EDP2939 is an investigational oral biologic consisting of EVs that we are developing for the potential treatment of inflammatory diseases. In vitro studies of EDP2939 in human and mouse cellular assays and in vivo models support its further development in the treatment of inflammatory diseases.

Preclinical Studies

In May 2021, we presented preclinical data for EDP2939 at the American Association of Immunologists Meeting. In the preclinical mechanism of action study, mice undergoing a delayed-type hypersensitivity (DTH) reaction against keyhole limpet hemagglutinin (KLH) were treated with EDP2939, EDP2939 in combination with different blocking antibodies, or with placebo. These data suggest that the pharmacological activity of EDP2939 may require the stimulation of both the TLR2 receptor and IL-10 receptor signaling, in addition to lymphocyte homing from the systemic circulation to the intestinal lymphoid tissue. In-vitro, EDP2939 induced TLR2-dependent release of IL-10. Fluorescent biodistribution analysis showed that EDP2939 was not detected outside the gastrointestinal tract. We also did not observe any apparent adverse safety or tolerability issues in these preclinical studies. We believe these




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data suggest that treatment with EDP2939 could result in broad-based resolution of inflammation and the establishment of immune homeostasis. EDP2939 is the first EV product candidate we have nominated in our inflammation program.

Phase 1/2 Clinical Trial

Dosing in our Phase 1/2, randomized, placebo-controlled trial has commenced and is being conducted in two parts. Part A will evaluate the safety and tolerability of EDP2939 in healthy volunteers. The primary endpoints of Part A (Phase 1) are safety endpoints, including adverse events, vital signs and safety laboratory tests. Part B (Phase 2) will evaluate the safety, tolerability and preliminary efficacy in adults with moderate psoriasis. The primary endpoint of Part B is the proportion of participants with moderate psoriasis achieving a PASI-50 response compared to placebo.

Part A (Phase 1) of the study is being conducted according to a randomized, placebo-controlled, participant-and investigator-blind, sponsor-open design. It includes up to three sequential, escalating multiple dose cohorts. Each cohort will comprise of 12 healthy volunteers receiving EDP2939 or placebo orally once a day for up to 10 days according to a 2:1 randomization. Prior to dose escalation, safety will be reviewed by a SRC, comprising members of the sponsor's clinical team and study investigators. Dose escalation to the next cohort may proceed once safety data from at least 10 participants who have completed the treatment period in the current cohort has been reviewed. An SRC meeting will also occur once safety data from at least 10 participants is available from Cohort 3. Cohort 1 of Part A of the study started dosing of healthy volunteers in January 2023, and no safety or tolerability concerns have been identified. Dose escalation proceeded to healthy volunteers in Cohort 2 after the dose level in Cohort 1 was reviewed by the SRC.

Part B (Phase 2) commenced dosing in psoriasis patients in February 2023, following the SRC review of initial dose level in Part A (Phase1). Part B (Phase 2) of the study is being conducted according to a randomized, double-blind, placebo-controlled design in participants with moderate plaque psoriasis. Participants in Part B will be randomly assigned in a 1:1 ratio to EDP2939 or matching placebo administered orally as a single capsule once a day for 16 weeks. We expect to report data from Part B (Phase 2) cohort in the second half of 2023.

Financing

In May 2022, we entered into a securities purchase agreement (the "Purchase Agreement") with the purchasers named therein (collectively, the "Purchasers"). Pursuant to the Purchase Agreement, we agreed to issue and sell to the Purchasers in a registered direct offering an aggregate of 54,246,358 shares of common stock, at a purchase price of $1.46 per share, pursuant to the 2021 Shelf Registration Statement and a related prospectus supplement filed with the SEC. The closing of the offering occurred on May 27, 2022. The placement generated gross proceeds of $79.2 million. There were no underwriting or placement fees associated with the transaction.

In July 2022, we entered into an "at-the-market" offering sales agreement with Cowen (the "2022 ATM") providing for the offering, issuance and sale of up to $75.0 million of common stock under the 2021 Shelf Registration Statement. We sold 2,799,400 shares of our common stock under the 2022 ATM during the year ended December 31, 2022. These shares were sold at a weighted average price per share of $2.10 for aggregate net proceeds of $5.9 million, after deducting commissions and offering costs. As of December 31, 2022, $69.1 million remained available to be sold under the 2022 ATM.

Debt Refinancing

In December 2022, we entered into a loan agreement with Horizon pursuant to which Horizon agreed to make term loans in an aggregate principal amount of up to $45.0 million, available to us on the closing date and we borrowed $45.0 million. Borrowings under the loan agreement are collateralized by substantially all of our personal property, excluding intellectual property, and we pledged our equity interests in our subsidiaries, subject to certain limitations with respect to our foreign subsidiaries. This loan carries interest only until February 2026, at which time it begins to amortize.

In connection with the entry into this new loan agreement, we repaid in full all outstanding indebtedness under our loan and security agreement with K2HV dated July 19, 2019, as amended, and K2HV terminated all of its interests except for 663,750 shares of our common stock subject to warrant. The aggregate principal amount of the loan outstanding at the time of repayment was $45.0 million. K2HV's security interest in our assets under the loan agreement were terminated in connection with our discharge of our indebtedness. See Note 8 - Loan and Security





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Agreements to our consolidated financial statements in this Annual Report on Form 10-K for additional information regarding our debt facility.

Chief Executive Officer Succession Plan

In August 2022, we announced the succession plan for Balkrishan "Simba" Gill, Ph.D., to transition from his role as our Chief Executive Officer and President to the role of Chairperson of our Board of Directors.

In January 2023, our Board of Directors asked Dr. Gill, and Dr. Gill agreed, to remain in his position as our Chief Executive Officer and President, and we halted the search for his successor. As a result, we anticipate that the leadership of our Board of Directors will remain unchanged, with Lord Ara Darzi continuing to serve as Chairperson.

Workforce Reduction

On January 31, 2023, our Board of Directors approved a plan to reduce our workforce by 48 employees, or approximately 45% of the our headcount as of such date (the "Workforce Reduction"), in order to preserve cash and prioritize investment in our core clinical programs. We estimate that we will incur aggregate charges in connection with the Workforce Reduction of approximately $2.7 million, which relate primarily to severance payments and related continuation of benefits costs, all of which are anticipated to result in future cash expenditures, along with the payment of accrued benefits, such as paid-time-off. We expect the majority of these costs to be incurred during the quarter ending March 31, 2023.

The foregoing estimates of the charges and expenditures that we expect to incur in connection with the Workforce Reduction, and the timing thereof, are subject to several assumptions and the actual amounts incurred may differ materially from these estimates. In addition, we may incur other charges or cash expenditures not currently contemplated due to unanticipated events that may occur, including in connection with the implementation of the Workforce Reduction.

ALJ Collaborations

In March 2021, we announced a strategic collaboration to develop and commercialize our lead inflammation product candidate, EDP1815, in the Middle East, Turkey, and Africa with ALJ. Under the terms of the agreement, we received an upfront payment from ALJ and we are primarily responsible for the development and manufacturing of EDP1815 worldwide, whilst ALJ will be primarily responsible for development, regulatory submissions and commercialization activities in the agreed-upon regions. ALJ and we will participate in a 50:50 profit share arrangement. See Note 2 - Summary of Significant Accounting Policies and Note 3 - ALJ Collaborative Agreement to our consolidated financial statements in this Annual Report on Form 10-K for additional information regarding the commercialization and license agreement with ALJ.

Global Events and Macroeconomic Conditions

Our operations have been and may in the future be impacted by several global events including, for example, changes to existing geopolitical dynamics, social and economic instability, and the impact of the COVID-19 pandemic, which have resulted in increased market volatility, changes to the labor market, sustained inflationary environment, increasing interest rates, financial institution failures and supply chain constraints. We have also seen adverse impacts from foreign currency exchange rates as a result of our UK operations, which have impacted our results. The ultimate extent the impact these global events and economic conditions will have on our businesses, operating results, cash flows, liquidity and financial condition will be driven primarily by the severity and duration of these conditions and the broad impact to the U.S. and global economies.




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Financial Operations Overview

Revenue

We have not generated any revenue since our inception and do not expect to generate any revenue from the sale of products in the near future, if at all. As discussed in Note 3 - ALJ Collaborative Agreement to our consolidated financial statements, we have entered into a collaboration agreement that will result in the recognition of $7.5 million of revenue upon the satisfaction of the performance obligation identified within the agreement. If our development efforts for our current product candidates or additional product candidates that we may develop in the future are successful and result in marketing approval, or if we enter into additional collaboration or license agreements with third parties, we may generate revenue in the future from a combination of product sales or payments from such collaboration or license agreements.

Operating Expenses

Our operating expenses since inception have consisted primarily of research and development ("R&D") activities and general and administrative ("G&A") costs.

Research and Development Expenses

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

•expenses incurred under agreements with third parties, including investigative sites, external laboratories and CROs, that conduct research, preclinical activities and clinical trials on our behalf;

•manufacturing process-development costs as well as technology transfer and other expenses incurred with CMOs that manufacture drug substance and drug product for use in our preclinical activities and any current or future clinical trials;

•salaries, benefits and other related costs, including stock-based compensation expense, for personnel in our research and development functions;

•expenses to acquire technologies to be used in research and development;

•costs of outside consultants, including their fees, stock-based compensation and related travel expenses;

•the cost of laboratory supplies and acquiring, developing and manufacturing preclinical and clinical trial materials;

•costs related to compliance with regulatory requirements; and

•facility-related expenses, which include direct depreciation costs and allocated expenses for rent and maintenance of facilities and other operating costs.

We expense R&D costs as incurred. We recognize external development costs based on an evaluation of the progress to completion of specific tasks using information provided to us by our vendors and our clinical investigative sites. Payments for these activities are based on the terms of the individual agreements, which may differ from the pattern of costs incurred, and are reflected in our consolidated financial statements as prepaid or accrued R&D expenses. Nonrefundable advance payments for goods or services to be received in the future for use in R&D activities are deferred and capitalized, even when there is no alternative future use for the research and development. The capitalized amounts are expensed as the related goods are delivered or the services are performed.

Our primary focus of R&D since inception has been building a platform to enable us to develop medicines based on an understanding of the gut-body network and to show potential clinical utility and develop the first set of clinical assets. Our platform and program expenses consist principally of costs, such as preclinical research, process development research, clinical and preclinical manufacturing activity costs, clinical development costs, licensing expense as well as an allocation of certain indirect costs, facility and office related expenses. We do not allocate personnel costs, which include salaries, discretionary bonus and stock-based compensation costs, as such costs are separately classified as R&D personnel costs.

R&D 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. Subject to obtaining appropriate funding, we expect that our R&D expenses will continue to increase in the foreseeable future as we continue to implement our business





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strategy and our ongoing clinical trials for our product candidates including EDP1815 and EDP2939, initiate additional clinical trials including potentially for EDP1815 and EDP2939, discover and develop additional product candidates, seek regulatory approvals for any products that successfully complete clinical trials, continue to source or potentially build manufacturing capabilities, hire additional R&D personnel and expand into additional therapeutic areas.

At this time, we cannot reasonably estimate or know the nature, timing and estimated costs of the efforts that will be necessary to complete the development of, and obtain regulatory approval for, any of our product candidates. We are also unable to predict when, if ever, material net cash inflows will commence from sales or licensing of our product candidates. This is due to the numerous risks and uncertainties associated with drug development, including without limitation the uncertainty of:

•our ability to add and retain key research and development personnel;

•our ability to successfully develop, obtain regulatory approval for, and then successfully commercialize, our product candidates;

•our ability to obtain regulatory approval to conduct registration trials;

•our successful enrollment in and completion of clinical trials;

•any delays in clinical trials, as a result of public health crises, such as the COVID-19 pandemic;

•global economic slowdown and market instability, including the impact from supply chain delays and increasing inflation and interest rates;

•the costs associated with the development of our current product candidates and/or any additional product candidates that we identify in-house or acquire through collaborations;

•our ability to discover, develop and utilize biomarkers to demonstrate target engagement, pathway engagement and the impact on disease progression of our product candidates;

•our ability to establish an appropriate safety profile with IND-enabling toxicology studies;

•our ability to establish and maintain agreements with CMOs and other entities for clinical trial supply and future commercial supply, if our product candidates are approved;

•the terms and timing of any collaboration, license or other arrangement, including the terms and timing of any milestone payments thereunder;

•our ability to obtain and maintain patent, trade secret and other intellectual property protection and regulatory exclusivity for our product candidates if and when approved;

•our receipt of marketing approvals from applicable regulatory authorities;

•our ability to commercialize products, if and when approved, whether alone or in collaboration with others; and

•the continued acceptable safety profiles of the product candidates following approval.

A change in any of these or other variables with respect to the development of any of our current or future product candidates would significantly change the costs, timing and viability associated with the development of that product candidate. We expect our research and development expenses to increase at least over the next several years as we continue to implement our business strategy, advance our current programs, expand our research and development efforts, seek regulatory approvals for any product candidates that successfully complete clinical trials, identify and develop additional product candidates, and incur expenses associated with hiring additional or retaining existing personnel to support our research and development efforts.





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General and Administrative Expenses

G&A expenses consist primarily of salaries and other related costs, including stock-based compensation, for personnel in our executive, finance, pre-commercial, corporate and business development, and administrative functions. G&A expenses also include legal fees relating to patent and corporate matters; professional fees for accounting, auditing, tax and administrative consulting services; insurance costs; administrative travel expenses; and facility-related expenses, which include direct depreciation costs and allocated expenses for rent and maintenance of facilities and other operating costs; and other costs associated with operating a public company including investor relations and board related fees and expenses.

Interest Expense, Net

During the years ended December 31, 2022 and 2021, interest expense, net consisted primarily of interest at the stated rate on borrowings under our loan and security agreements, amortization of deferred financing costs and interest expense related to the accretion of debt discount offset by interest earned on institutional money market instruments.

We anticipate that the interest expense on our outstanding loan will increase in the near term, if and as interest rates rise in response to actions taken by the U.S. Federal Reserve. We expect that interest income earned on our money market accounts may increase in response to rising interest rates; however the net impact is uncertain given our fluctuating cash/money market balances.

Loss on Extinguishment of Debt

Loss on extinguishment of debt for the year ended December 31, 2022 reflects the difference between the reacquisition cost of the new debt with Horizon, inclusive of the fair value of the warrant issued to purchase our common shares at $1.94 per share, and the carrying amount of the existing debt in addition to lender fees.

Other Miscellaneous Income, Net

For the year ended December 31, 2022, other miscellaneous income, net consists of government R&D tax credits related to our operations in the UK, offset by foreign currency exchange losses and changes in the fair value of common stock warrants.

Income Taxes

Income tax expense primarily relates to tax expense at our UK subsidiary.

Since our inception in 2014, we have not recorded any U.S. federal or state income tax benefits for the net losses we have incurred in each year or our earned research and development tax credits, due to our uncertainty of realizing a benefit from those items.





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Results of Operations

Comparison of Years Ended December 31, 2022 and 2021



Our statement of operations for the years ended December 31, 2022 and 2021 (in
thousands):
                                      Year Ended December 31,
                                       2022              2021          Change
Operating expenses:
Research and development          $      78,554      $   83,643      $ (5,089)
General and administrative               29,912          31,753        (1,841)
Total operating expenses                108,466         115,396        (6,930)
Loss from operations                   (108,466)       (115,396)        6,930
Other income (expense):
Interest expense, net                    (4,672)         (3,612)       (1,060)
Loss on extinguishment of debt             (520)         (3,226)        2,706
Other miscellaneous income, net              61             486          (425)
Total other expenses, net                (5,131)         (6,352)        1,221
Loss before income taxes               (113,597)       (121,748)        8,151
Income tax expense                         (930)           (428)         (502)
Net loss                          $    (114,527)     $ (122,176)     $  7,649


Net Loss

The net loss was $114.5 million for the year ended December 31, 2022, compared to $122.2 million for the year ended December 31, 2021. The lower net loss of $7.6 million was the result of a decrease of $6.9 million in total operating expenses, and a $2.7 million lower loss on the extinguishment of debt in the current year, offset by a $1.1 million increase in net interest expense, a $0.4 million decrease in other miscellaneous income and a $0.5 million increase in income taxes. Of our total operating expenses, R&D expenses decreased by $5.1 million while G&A expenses decreased by $1.8 million.

Research and Development Expenses (in thousands):


                                                Year Ended December 31,
                                                   2022                2021         Change
Inflammation programs                     $      39,030             $ 37,394      $  1,636
Personnel costs                                  18,845               22,030        (3,185)
Platform expenses                                13,350               13,412           (62)
Stock-based compensation                          7,140                8,004          (864)
Oncology programs                                   189                2,803        (2,614)
Total research and development expenses   $      78,554             $ 83,643      $ (5,089)

R&D expenses were $78.6 million for the year ended December 31, 2022, compared to $83.6 million for the year ended December 31, 2021. The overall decrease of $5.1 million was driven primarily by a $3.2 million decrease in personnel costs due to the absence of discretionary bonus expense in 2022, a decrease of $0.9 million stock-based compensation, and $2.6 million lower costs as a result of the completion of the oncology program related spend. These decreases were partially offset by a $1.6 million net increase in inflammation programs spending, which was driven by the ramp up of the EDP1815 Phase 2 trial in atopic dermatitis, initiation of EDP2939 extracellular vesicles programs, and a KLH trial for EDP1815. These increases were partially offset by a decrease in spending upon the completion of an EDP1815 Phase 2 trial in psoriasis patients, EDP1815 Phase 1b trials, and the closeouts of the EDP1867 and EDP1815 COVID-19 programs. Overall, we expect to continue to closely control spending in research and development, as appropriate, prioritizing our clinical trials for our lead product candidates EDP1815 and EDP2939 and, as resources permit, potentially expand into additional therapeutic areas, continue discovery and development efforts for additional potential product candidates, and seek to increase manufacturing capabilities.




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General and Administrative Expenses (in thousands):


                                                   Year Ended December 31,
                                                      2022                2021         Change
Personnel costs                              $      11,342             $ 11,769      $   (427)
Stock-based compensation                             8,018                7,842           176
Professional fees                                    5,833                6,714          (881)
Facility costs, office expense and other             4,719                5,428          (709)
Total general and administrative expenses    $      29,912             $ 31,753      $ (1,841)

G&A expenses were $29.9 million for the year ended December 31, 2022, compared to $31.8 million for the year ended December 31, 2021. The decrease of $1.8 million was primarily driven by a $0.9 million decrease in general and administrative professional fees (including lower consulting fees offset by increased investment in intellectual property), a $0.7 million decrease in facilities and related spend given focus on cost controls, and a $0.4 million decrease in personnel-related costs partially driven by the absence of discretionary bonus expense in 2022, partially offset by a $0.2 million increase in stock-based compensation.

Total Other Expense, Net

Total other expense, net for the year ended December 31, 2022 was $5.1 million compared to $6.4 million for the year ended December 31, 2021. This decrease of $1.2 million was primarily driven by a $2.7 million lower loss on the extinguishment of debt realized in 2022 compared to 2021, offset by increased net interest expense of $1.1 million resulting from both higher current year average debt balances and interest rates, and a $0.4 million losses on foreign currencies.





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Liquidity and Capital Resources

We were incorporated and commenced operations in 2014. Since our incorporation, we have devoted substantially all of our resources to developing preclinical and clinical product candidates, building our intellectual property portfolio and process development and manufacturing function, business planning, raising capital and providing general and administrative support for these operations. To date, we have financed our operations primarily with the proceeds from issuance of our common stock combined with proceeds from previous sales of our convertible preferred stock to our equity investors and borrowings under loan and security agreements. From our inception through December 31, 2022, we have received gross proceeds of $520.1 million from such transactions, which includes a net $45.0 million borrowed under debt facilities. As of December 31, 2022, we had cash and cash equivalents of $47.9 million and an accumulated deficit of $529.2 million.

In February 2023, we released interim data from the first three cohorts of our ongoing Phase 2 trial of EDP1815 in atopic dermatitis patients. Cohorts one, two and three failed to meet the trial's primary endpoint, which is the proportion of patients who achieve an outcome of an EASI-50 response, compared to placebo at week 16. In connection with this data, we implemented cost reduction initiatives, including a reduction in workforce of 48 employees, or approximately 45% of our headcount as of the date of the reduction, in order to preserve cash and prioritize investment in our core clinical programs. We estimate that we will incur aggregate charges in connection with the Workforce Reduction of approximately $2.7 million, which relate primarily to severance payments and related continuation of benefits costs, all of which are anticipated to result in future cash expenditures, along with the payment of accrued benefits (such as paid-time-off). We expect the majority of these costs to be incurred during the quarter ending March 31, 2023. The Workforce Reduction and other cost savings actions being implemented are expected to extend our cash runway into the third quarter of 2023.

We evaluated whether there are conditions and events, considered in the aggregate, that raise substantial doubt about our ability to continue as a going concern within one year after the date that the consolidated financial statements are issued. We incurred net losses of approximately $114.5 million and $122.2 million for the years ended December 31, 2022 and 2021, respectively. We have incurred losses and generated negative operating cash flows since our inception and anticipate that we will continue to incur losses for at least the next several years. The transition to profitability is dependent upon the successful development, approval, and commercialization of our products and product candidates and the achievement of a level of revenues adequate to support our cost structure. Based on our current operating plan, we believe that our cash and cash equivalents as of December 31, 2022 will not be sufficient to fund operations and capital expenditures for at least the twelve months following the filing of this Annual Report on Form 10-K, and we will need to obtain additional funding. Until such time, if ever, as we can generate revenue from product sales, we intend to pursue strategic partnerships, licensing arrangements and collaborations, and obtain additional funding through our available financing sources, which may include additional public offerings of common stock and private financing of debt or equity. There can be no assurance that we will be successful in pursuing any such partnerships, licensing arrangements or collaborations, or that any such financings will be obtained on terms acceptable to us, if at all. If we are unable to raise additional capital in sufficient amounts or on terms acceptable to us, we will have to significantly delay, scale back or discontinue our research and development programs, future commercialization efforts, or operations. Our beliefs about our ability to fund operations is based on estimates that are subject to risks and uncertainties. If actual results are different from our estimates, we may need to seek additional funding, if it is available, sooner or on less desirable terms than would otherwise be expected.

We anticipate capital expenditures for 2023 to be minimal.

Funding Requirements

We have incurred losses and cumulative negative cash flows from operations since our inception. We anticipate that we will continue to incur significant losses for at least the next several years. We expect that our research and development and general and administrative expenses will continue to increase. As a result, we will need additional capital to fund our operations, which we may raise through a combination of the sale of equity, debt financings, or other sources, including potential collaborations.

We expect our expenses to increase substantially in connection with our ongoing development activities related to the initiation of clinical studies and preclinical work on additional monoclonal microbial and extracellular vesicle product candidates, which are still in development, and our follow-on therapeutics and other programs. In addition, we expect to incur additional costs associated with operating as a public company. We anticipate that our expenses will increase substantially if and as we:





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•continue our clinical trials, including for EDP1815 and EDP2939;

•advance the clinical development of additional product candidates;

•conduct research and continue preclinical development of potential product candidates;

•make strategic investments in manufacturing capabilities, including potentially planning and building a commercial manufacturing facility;

•maintain our current intellectual property portfolio and opportunistically acquire complementary intellectual property;

•seek to obtain regulatory approvals for our product candidates;

•potentially establish a sales, marketing and distribution infrastructure and scale-up manufacturing capabilities to commercialize any products for which we may obtain regulatory approval;

•add clinical, scientific, operational, financial and management information systems and personnel, including personnel to support our product development and potential future commercialization efforts and to support our operations as a public company; and

•experience any delays or encounter any issues with any of the above, including but not limited to failed studies or trials, complex results, safety issues or other regulatory or personnel challenges.

As of December 31, 2022, our principal source of liquidity is cash and cash equivalents, which totaled $47.9 million. Our cash and cash equivalents are maintained at financial institutions in amounts that exceed federally insured limits. We expect that our existing cash and cash equivalents as of December 31, 2022 will enable us to fund our planned operating expenses and capital expenditure requirements into the third quarter of 2023. Based on our current operating plan, we believe that our cash and cash equivalents will not be sufficient to fund operations and capital expenditures for at least the twelve months following the filing of this Annual Report on Form 10-K, and we will need to obtain additional funding. 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. Our forecast is based on assumptions that may prove to be wrong, and we may use our available capital resources sooner than we currently expect. Due to the uncertainty in securing additional funding, and the insufficient amount of cash and cash equivalent resources as of December 31, 2022, we have concluded that substantial doubt exists with respect to our ability to continue as a going concern within one year after the date of the filing of this Annual Report on Form 10-K.

Because of the numerous risks and uncertainties associated with the development of our product candidates, including EDP1815 and EDP2939, any additional product candidates or any follow-on programs, and because the extent to which we may enter into further partnerships, collaborations or licensing arrangements with third parties for the development of these product candidates is unknown, we are unable to estimate the amounts of increased capital outlays and operating expenses associated with completing the research and development of our product candidates. Our future capital requirements for our technology platform or our other programs will depend on many factors, including:

•the costs, progress and results of our clinical trials, including of EDP1815 and EDP2939;

•the cost of manufacturing clinical supplies of our product candidates;

•the scope, progress, results and costs of preclinical development, including laboratory testing and studies, for any other potential product candidates;

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

•the costs and timing of future commercialization activities, including manufacturing, marketing, sales and distribution, for any of our product candidates for which we receive marketing approval;

•the revenue, if any, received from commercial sales of our product candidates for which we receive marketing approval;

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

•the effect of competing technological and market developments; and




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•the extent to which we acquire or invest in businesses, products and technologies, including entering into licensing or collaboration arrangements for product candidates, although we currently have no additional commitments or agreements to complete any such acquisitions or investments in businesses.

Identifying potential product candidates and conducting preclinical testing and clinical trials is a time consuming, expensive and uncertain process that takes years to complete. We may never generate the necessary data or results required to obtain marketing approval and achieve product sales. In addition, our product candidates, if approved, may not achieve commercial success. Our commercial revenues, if any, will be derived from sales of products that we do not expect to be commercially available for many years, if ever. Accordingly, we will need to obtain substantial additional funds to achieve our business objectives.

Adequate additional funds may not be available to us on acceptable terms, or at all. To the extent that we raise additional capital through the sale of equity or convertible debt securities, the ownership interest of existing stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of common stockholders. Additional 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 capital expenditures or declaring dividends and may require or involve the issuance of warrants, which could potentially dilute the ownership interest of existing stockholders. The terms of our loan and security agreement with Horizon preclude us from paying dividends on our equity securities without their consent. If we lack sufficient capital to expand our operations or otherwise capitalize on our business opportunities, our business, financial condition and results of operations would be materially adversely affected.

If we raise additional funds through collaborations, partnerships, strategic alliances 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 when needed, we may be required to delay, limit or terminate our product development programs or any future commercialization efforts or grant rights to develop and market product candidates to third parties that we would otherwise prefer to develop and market ourselves.

Financing

We are a development stage company and have not generated any revenue. All of our product candidates are in early clinical or preclinical development. Our ability to generate product revenue sufficient to achieve profitability will depend heavily on the successful development and eventual commercialization of one or more of our product candidates. Since our inception, we have incurred significant operating losses and we continue to incur significant research and development and other expenses related to our ongoing operations. In addition, if we obtain marketing approval for any of our product candidates, we expect to incur significant commercialization expenses related to product manufacturing, marketing, sales and distribution.

As a result, we will need additional financing to support our continuing operations. Until such time as we can generate significant revenue from product sales, if ever, we expect to finance our operations through a combination of public or private equity or debt financings or other sources, which may include collaborations with third parties. Adequate additional financing may not be available to us on acceptable terms, or at all. Additionally, our ability to raise capital may be impacted by global macroeconomic conditions including as a result of international political conflict, supply chain issues and rising inflation and interest rates. Our inability to raise capital as and when needed would have a negative impact on our financial condition and our ability to pursue our business strategy. We will need to generate significant revenue to achieve profitability, and we may never do so.

We also anticipate continuing increases in U.S. interest rates will result in both higher interest expense and potentially interest income depending upon our invested cash balance, but we are unable to anticipate with any certainty the future net effect to our consolidated net loss and resulting cash flows from operating activity.

Because of the numerous risks and uncertainties associated with drug development, we are unable to 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 revenue from 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.





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Equity Financing

In June 2019, we filed a Registration Statement on Form S-3 (File No. 333-231911) (the "2019 Shelf Registration Statement") with the SEC in relation to the registration of common stock, preferred stock, debt securities, warrants and/or units of any combination thereof in the aggregate amount of up to $200 million for a period of up to three years from the date of its effectiveness on June 6, 2019. We simultaneously entered into an "at-the-market" offering sales agreement with Cowen and Company, LLC, as sales agent ("Cowen") (the "2019 ATM") providing for the offering, issuance and sale of up to $50.0 million of common stock under the 2019 Shelf Registration Statement.

For the year ended December 31, 2022, we sold no shares of common stock under the 2019 ATM. For the year ended December 31, 2021, we issued 139,734 common shares under the 2019 ATM with offering prices ranging between $12.54 and $13.17 per share for net proceeds of $1.7 million. The 2019 Shelf Registration Statement expired in June 2022, and we terminated the 2019 ATM in July 2022.

In January 2021, we entered into a stock purchase agreement with ALJ Health Care & Life Sciences Company Limited ("ALJ Health Care"), pursuant to which on February 2, 2021, ALJ Health Care purchased $7.5 million of our common stock in a private placement at a purchase price of $15.00 per share. The sale of these 500,000 shares was not registered under the Securities Act.

In February 2021, we sold 5,175,000 shares of our common stock in an underwritten public offering at a public offering price of $15.00 per share, including the underwriters' exercise of their option to purchase 675,000 shares to cover over-allotment, generating gross proceeds of $77.6 million and net proceeds of $73.0 million, after deducting underwriting discounts and commissions, exclusive of other offering expenses payable by us.

In August 2021, we filed a Registration Statement on Form S-3 (File No. 333-259005) (the "2021 Shelf Registration Statement") with the SEC in relation to the registration of common stock, preferred stock, debt securities, warrants and/or units of any combination thereof in the aggregate amount of up to $200 million for a period of up to three years from the date of its effectiveness on August 30, 2021.

In May 2022, we entered into a securities purchase agreement (the "Purchase Agreement") with the purchasers named therein (collectively, the "Purchasers"). Pursuant to the Purchase Agreement, we agreed to issue and sell to the Purchasers in a registered direct offering an aggregate of 54,246,358 shares of common stock, at a purchase price of $1.46 per share, pursuant to the 2021 Shelf Registration Statement and a related prospectus supplement filed with the SEC. The closing of the offering occurred on May 27, 2022. The placement generated gross proceeds of $79.2 million. There were no underwriting or placement fees associated with the transaction.

In July 2022, we entered into an "at-the-market" offering sales agreement with Cowen (the "2022 ATM") providing for the offering, issuance and sale of up to $75.0 million of common stock under the 2021 Shelf Registration Statement. We sold 2,799,400 shares of our common stock under the 2022 ATM during the year ended December 31, 2022. These shares were sold at a weighted average price per share of $2.10 for aggregate net proceeds of $5.9 million, after deducting commissions and offering costs. As of December 31, 2022, $69.1 million remained available to be sold under the 2022 ATM.

See "Liquidity and Capital Resources" and Note 11 - Stockholders' (Deficit) Equity to our consolidated financial statements in this Annual Report on Form 10-K for additional information regarding our equity financing.



Debt Financing
K2 HealthVentures LLC Loan Termination

In July 2019, we entered into a loan and security agreement with K2HV, under which K2HV agreed to extend term loans of up to $45.0 million in three tranches. The initial tranche of $20.0 million was funded in July 2019. The second tranche of $10.0 million was funded in July 2020. The availability of the third tranche of $15.0 million expired in January 2021. The facility was amended in June 2021 (the "Amended Credit Facility"), to supersede the expired $15.0 million third tranche commitment with a new $15.0 million fourth tranche commitment, which we drew down in June 2021. The Amended Credit Facility resulted in a debt extinguishment for accounting purposes, and we recorded a loss on the extinguishment of debt of $3.2 million in the third quarter of 2021, equaling the difference between the fair value for reacquisition of the new debt and the carrying amount of the existing debt.




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In connection with the Amended Credit Facility, we issued to K2 HealthVentures Equity Trust LLC, an affiliate of K2HV, a warrant to purchase up to 139,770 shares of our common stock (the "Warrant") at a Warrant Price (as defined in the Warrant) of $13.30 per share. In addition, we provided K2HV the option (the "Conversion Option"), exercisable at any time, to convert at a Conversion Price (as defined in the Amended Credit Facility) of $13.30 per share up to $5.0 million of loan principal outstanding into up to 375,940 shares of our common stock.

During our debt covenant compliance reviews applicable to periods in the third quarter of 2022, we identified certain Events of Default (as defined in the Amended Credit Facility) resulting from non-compliance with certain provisions of the Amended Credit Facility. Under the Amended Credit Facility, Events of Default may have entitled the lenders to default interest, the ability to terminate the facility and the ability to accelerate repayment of any outstanding loans in full.

On November 14, 2022, we and K2HV entered into a Waiver of Specific Defaults and Modification of Terms letter (the "Modification Letter") to the Amended Credit Facility whereby we agreed, among other things, to accelerate the Final Payment of $2.2 million such that it became payable and was paid on December 12, 2022, to amend and restate the Warrant to change the Warrant Price to $2.00 per share and increase the number of shares subject to the Warrant to 663,750; and with respect to the Conversion Option, restate the Conversion Price to $2.00 per share, such that K2HV could have converted up to $5.0 million of loan principal outstanding into up to 2,500,000 shares of our common stock. The changes made to the agreement terms were classified as a modification of the Amended Credit Facility. We concluded that the Warrant and the Conversion Option met the criteria to be classified within equity and as such the modification of the Warrant and Conversion Option resulted in additional discounts of $0.9 million and $1.5 million, respectively, recorded against the carrying amount of the outstanding debt, with an offset to additional paid in capital.

In connection with the entry into the new loan agreement with Horizon, discussed below, we repaid in full all outstanding indebtedness under the Amended Credit Facility, and K2HV terminated all of its interests thereunder, except for the 663,750 shares of our common stock subject to the Warrant. The aggregate principal amount of the loan outstanding at the time of repayment was $45.0 million. K2HV's security interest in our assets under the loan agreement were terminated in connection with our discharge of our indebtedness thereunder. We did not incur any penalties, but did incur a prepayment fee of $0.4 million and a loss on the extinguishment of debt of $0.5 million as a result of the foregoing.

Horizon Technology Finance Corporation Loan and Security Agreement

In December 2022, we entered into a loan agreement with Horizon pursuant to which Horizon agreed to make term loans in an aggregate principal amount of up to $45.0 million, available to us on the closing date, and we borrowed $45.0 million. Borrowings under the loan agreement are collateralized by substantially all of our personal property, excluding intellectual property, and we pledged our equity interests in our subsidiaries, subject to certain limitations with respect to our foreign subsidiaries.

Interest on the outstanding loan balance will accrue at a variable annual rate equal to the greater of (i) 11% and (ii) rate of interest noted in The Wall Street Journal, Money Rates section, as the "Prime Rate" plus the "Loan Rate Spread" as defined in the loan agreement. We are required to make interest-only payments on the loans on the stub period date (January 1, 2023) and for the first thirty-six monthly payment dates prior to when the loans are scheduled to begin amortizing on February 1, 2026. Beginning on February 1, 2026, we must pay twenty-four equal consecutive monthly installment payments repaying $35.0 million of the principal, plus interest on all outstanding balance until the loans mature on January 1, 2028 (the "Maturity Date"). The remaining $10.0 million of principal is due and payable on the Maturity Date. At our option, we may prepay the loans in whole, subject to a prepayment fee of 3% of the amount prepaid if prepaid on or before the Amortization Date, or if the prepayment occurs after less than 12 months after Amortization Date, 2% of the amount prepaid, and if more than 12 months after the Amortization Date but before the Maturity Date, 1%. A final payment equal to 4.25% of the principal borrowed on the closing date is due on the Maturity Date (or upon repayment in full of principal, if earlier).

Upon the entry into the loan agreement, we were required to pay Horizon a commitment fee of $0.5 million, as well as other customary fees and expenses. The loan agreement contains customary representations, warranties and covenants and also includes customary events of default, including payment defaults, breaches of covenants, change of control and occurrence of a material adverse effect. Upon the occurrence and continuation of an event of default, a default interest rate of an additional 5% per annum may be applied to the outstanding loan balances, and Horizon may declare all outstanding obligations immediately due and payable and exercise all of their rights and




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remedies as set forth in the loan agreement and under applicable law. Our subsidiary, Evelo Biosciences Security Corporation, may maintain cash or cash equivalents so long as we satisfy certain liquidity requirements. As of December 31, 2022, we were in compliance with all covenants under the Loan Agreement.

In connection with the entry into the loan agreement, we also issued to Horizon warrants to purchase up to an aggregate 463,915 shares of our common stock, with an exercise price of $1.94 per share. The warrants are exercisable immediately and expire on December 15, 2032, provided that, under certain circumstances, the warrants may terminate and expire earlier in connection with the closing of certain acquisition transactions involving us. The warrants provide that Horizon may elect to exercise the warrant on a net "cashless" basis at any time prior to the expiration thereof. The fair market value of one share of our common stock in connection with any cashless exercise shall be the closing price or last sale price per share of our common stock on a nationally recognized securities exchange, inter-dealer quotation system or over-the-counter market on which our common stock is traded on the business day immediately prior to the date the holder elects to exercise the warrants on a cashless basis.

See Note 8 - Loan and Security Agreements to our consolidated financial statements in this Annual Report on Form 10-K for additional information regarding our debt facility.

License and Manufacturing Agreements

See Part I, Item 1. "License and Manufacturing Agreements" for additional information about our license and manufacturing agreements.

Cash Flows

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



                                                                   Year Ended December 31,
                                                                2022                      2021
Cash used in operating activities                       $      (101,235)            $      (96,725)
Cash used in investing activities                                  (622)                    (1,481)
Cash provided by financing activities                            81,655                     97,540
Effect of exchange rate changes on cash and cash
equivalents                                                        (454)                         -
Net decrease in cash, cash equivalents and restricted
cash                                                    $       (20,656)            $         (666)


Operating Activities

Net cash used in operating activities for the year ended December 31, 2022, was $101.2 million, driven primarily by our net loss of $114.5 million which originates from investments in research and clinical study costs to advance our programs, as well as general and administrative costs which include costs to operate as a public company. This net loss figure is reduced by non-cash charges consisting of stock-based compensation expense of $15.2 million, depreciation expense of $2.1 million, lease expense of $2.9 million, interest expense of $1.5 million, loss on extinguishment of debt of $0.5 million, and foreign currency losses of $0.4 million. The change in operating assets and liabilities, primarily the pay-down of liabilities including the operating lease for the Company's office, account for $9.7 million of cash used in operations.

We anticipate continuing increases in U.S. interest rates will result in both higher interest income and interest expense, but we are unable to anticipate with any certainty the future net effect to our consolidated net loss and resulting cash flows from operating activity.

Net cash used in operating activities for the year ended December 31, 2021, was $96.7 million. Our net loss of $122.2 million included the following more significant non-cash charges: $15.8 million of stock-based compensation expense; a $3.2 million loss on extinguishment of debt; $2.2 million of depreciation expense; and $1.8 million of lease expense. The net decrease in operating assets and liabilities was $2.1 million.

Investing Activities

Net cash used in investing activities for the year ended December 31, 2022 and 2021 was $0.6 million and $1.5 million, respectively, primarily due to the purchase of capital equipment.





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Financing Activities

Net cash provided by financing activities for the year ended December 31, 2022 was $81.7 million, primarily due to $84.5 million of proceeds from issuance of common stock, $0.2 million of proceeds from the issuance of common stock in connection with the exercise of options, and $44.5 million from the issuance of long-term debt under the Horizon loan and security agreement, offset by $47.6 million full repayment of our outstanding indebtedness under our loan and security agreement with K2HV.

Net cash provided by financing activities for the year ended December 31, 2021 was $97.5 million, primarily due to $81.8 million of proceeds from issuance of common stock, $14.8 million from the issuance of long-term debt under the K2HV Amended Credit Facility, and $1.0 million of proceeds from the issuance of common stock in connection with the exercise of options.

Contractual Obligations

We have entered into arrangements that contractually obligate us to make payments that will affect our liquidity and cash flows in future periods. Our contractual obligations primarily consist of our obligations under operating leases and spending obligations related to one of our manufacturing agreements. The aggregate amount of future operating lease obligations over the term of our leases is $8.6 million as of December 31, 2022. We currently have a contractual arrangement in place with one of our CMOs, under which the remaining aggregate amount of future spending obligations is €3.9 million, consisting of €1.5 million annually during each of 2023 and 2024, and €0.9 million on or before March 1, 2025. For additional information on our leases and spending obligations, refer to our notes to the consolidated financial statements.

Critical Accounting Policies and Use of Estimates

Our management's discussion and analysis of financial condition and results of operations are based on our consolidated financial statements which are prepared in accordance with generally accepted accounting principles, or GAAP, in the United States of America. The preparation of our consolidated financial statements and related disclosures requires us to make estimates and assumptions that affect the reported amount of assets, liabilities, revenue, costs and expenses, and related disclosures. We believe that the estimates and assumptions involved in the accounting policies described below may have the greatest potential impact on our consolidated financial statements and, therefore, consider these to be our critical accounting policies. We evaluate our estimates and assumptions on an ongoing basis using historical experience, known trends and events and various other factors that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Our actual results may differ from these estimates under different assumptions and conditions.

Accrued Research and Development Expenses

As part of the process of preparing our consolidated financial statements, we are required to estimate our accrued research and development expenses. This process involves reviewing open contracts and purchase orders, communicating with our personnel to identify services that have been performed on our behalf and estimating the level of service performed and the associated costs incurred for the services when we have not yet been invoiced or otherwise notified of the actual costs. The majority of our service providers invoice us in arrears for services performed, on a pre-determined schedule or when contractual milestones are met; however, some require advanced payments. We make estimates of our accrued expenses as of each balance sheet date in our consolidated financial statements based on facts and circumstances known to us at that time. Examples of estimated accrued research and development expenses include fees paid to:

•CROs in connection with performing research services on our behalf including, but not limited to, clinical trials and preclinical studies;

•investigative sites and other providers in connection with clinical trials and preclinical studies;

•other research and development service providers such as academic institutions and laboratory services providers in connection with discovery, preclinical and clinical development activities; and

•vendors related to product manufacturing, development and distribution of clinical supplies.

We base our expenses related to clinical trials and preclinical studies on our estimates of the services received and efforts expended pursuant to quotes and contracts with multiple CROs, investigative sites, laboratories and other providers that conduct and manage those studies on our behalf. The financial terms of these agreements are





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subject to negotiation, vary from contract to contract and may result in uneven payment flows. There may be instances in which payments made to our vendors will exceed the level of services provided and result in a prepayment of the clinical expense. Payments under some of these contracts depend on factors such as the successful enrollment of patients and the completion of milestones. In accruing service fees, we estimate the time period over which services will be performed, enrollment of patients, number of sites activated and the level of effort to be expended in each period. If the actual timing of the performance of services or the level of effort varies from our estimate, we adjust the accrual or amount of prepaid expense accordingly. Although we do not expect our estimates to be materially different from amounts actually incurred, our understanding of the status and timing of services performed relative to the actual status and timing of services performed may vary and may result in us reporting amounts that are too high or too low in any particular period. To date, we have not made any material adjustments to our prior estimates of accrued research and development expenses.

Stock-Based Compensation

We measure stock options and other stock-based awards granted to employees and directors based on the fair value on the date of grant and recognize the corresponding compensation expense of those awards over the requisite service period, which is generally the vesting period of the respective award. Generally, we issue stock options and restricted stock awards with only service-based vesting conditions and record the expense for these awards using the straight-line method, adjusting for pre-vesting forfeitures in the period in which the forfeitures occur. We measure stock-based awards granted to consultants and non-employees based on the fair value of the award on the date of the grant. Compensation expense is recognized over the period during which services are rendered by such consultants and non-employees until completed.

We estimate the fair value of each stock option grant using the Black-Scholes option-pricing model. Use of this model requires that we make assumptions as to the volatility of our common stock, the expected term of our stock options, the risk-free interest rate for a period that approximates the expected term of our stock options, and our expected dividend yield. Prior to May 2018, we were a privately-held company with limited operating history and no company-specific historical and implied volatility information and accordingly, we estimate our expected volatility based on the historical volatility of a group of publicly traded peer companies. We expect to continue to do so until such time as we have adequate historical data regarding the volatility of our traded stock price. We use the simplified method prescribed by SEC Staff Accounting Bulletin No. 107, Share-Based Payment, to calculate the expected term of options granted to employees and directors. We base the expected term of options granted to consultants and non-employees on the contractual term of the options. We determine the risk-free interest rate by reference to the U.S. Treasury yield curve in effect at the time of grant of the award for time periods approximately equal to the expected term of the award. Expected dividend yield is based on the fact that we have never paid cash dividends and do not expect to pay any cash dividends in the foreseeable future.

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