You should read the following discussion and analysis of our financial condition and results of operations together with our condensed consolidated financial statements and related notes included elsewhere in this Quarterly Report on Form 10-Q. This discussion contains forward-looking statements that involve risks and uncertainties, including those described in the section titled "Special Note Regarding Forward Looking Statements." Our actual results and the timing of selected events could differ materially from those discussed below. Factors that could cause or contribute to such differences include, but are not limited to, those identified below and those set forth under the section titled "Risk Factors" included elsewhere in this report.

Overview

We are a clinical stage biopharmaceutical company pioneering immuno-neurology, a novel therapeutic approach for the treatment of neurodegeneration. Immuno-neurology targets immune dysfunction as a root cause of multiple pathologies that are drivers of degenerative brain disorders. We are developing therapies designed to counteract these pathologies simultaneously by restoring healthy immune function to the brain. Supporting our scientific approach, our research and drug discovery platform enables us to advance a broad portfolio of product candidates, validated by human genetics, which we believe will improve the probability of technical success over shorter development timelines. As a result, we have identified over 100 immune system targets. Three product candidates, latozinemab (also referred to as AL001), AL002, and AL101 are in clinical development, and we continue to develop our preclinical and research pipeline. We are focusing our development resources on latozinemab in frontotemporal dementia (FTD) and AL002 and AL101 in Alzheimer's disease (AD). We are advancing our clinical product candidates and research pipeline with our existing resources and in collaboration with our partners, GSK and AbbVie.

In July 2021, we entered into a Collaboration and License Agreement with GSK (GSK Agreement) to collaborate on the global development and commercialization of progranulin-elevating monoclonal antibodies, including latozinemab and AL101.

Latozinemab modulates progranulin (PGRN), a key regulator of immune activity in the brain with genetic links to multiple neurodegenerative disorders. Latozinemab is in development to treat FTD, a severe, rapidly progressing neurodegenerative disorder that affects 50,000 to 60,000 people in the United States and roughly 110,000 people in the European Union.

Latozinemab is currently being studied in a global pivotal Phase 3 trial, INFRONT-3, for the potential treatment of adults at risk for or with symptomatic FTD due to a progranulin gene mutation (FTD-GRN), and in the Phase 2 INFRONT-2 trial in FTD patients with a C9orf72 genetic mutation (FTD-C9orf72). We remain on track to engage with regulatory authorities in mid-2023 regarding the INFRONT-3 trial of latozinemab. The purpose of the meeting is to discuss statistical analysis plans based on emerging knowledge in the field that may enable us to complete the pivotal INFRONT-3 clinical trial with fewer patients and/or a shorter treatment duration. We are targeting an INFRONT-3 data readout in early 2025 with the potential for a Biologics License Application (BLA) filing in late 2025 subject to regulatory discussion outcomes. In prior clinical studies, latozinemab demonstrated elevation of progranulin levels back to the normal range and early signals of exploratory biomarker and clinical activity. Latozinemab has been well tolerated in healthy volunteers and FTD-GRN and FTD-C9orf72 patients in our Phase 1a, Phase 1b, and Phase 2 clinical trials.

We previously presented data for latozinemab from our ongoing open-label Phase 2 clinical trial, INFRONT-2 in patients with FTD-GRN in 2021, and in March 2022, we presented additional data from the INFRONT-2 trial of latozinemab in FTD patients with FTD-C9orf72. We intend to provide additional data updates on the entire FTD-C9orf72 cohort in the INFRONT-2 Phase 2 clinical trial of latozinemab in the second half of 2023.

AL101, the second product candidate in our PGRN portfolio, is designed to elevate progranulin levels, similar to latozinemab, for use in the treatment of larger indications including Alzheimer's disease and Parkinson's disease. We and GSK plan to initiate a global Phase 2 clinical trial in early AD. We anticipate that GSK will conduct the phase 2 trial for AL101 in AD.

Our AL002 product candidate targets Triggering Receptor Expressed on Myeloid cells 2 (TREM2) to increase the functionality of TREM2 signaling and enhance microglia cell activation. In October 2017, we entered into the Co-Development and Option Agreement with AbbVie, and we are currently developing AL002 for the treatment of Alzheimer's disease in collaboration with AbbVie.

In January 2023, the first patient was enrolled and dosed in a long-term extension (LTE) of our INVOKE-2 Phase 2 clinical trial. In February 2023, we and AbbVie amended the AbbVie agreement (AbbVie Amendment), which resulted in our receiving a $17.8 million milestone payment in March 2023 for the dosing of the first patient in an LTE trial. Under the terms of the AbbVie Amendment, the Company will be eligible to earn up to an additional $12.5 million to support the



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enrollment of additional patients in the ongoing INVOKE-2 trial to replace discontinuations. We are on track to complete enrollment in the trial in the third quarter of 2023, with top-line data expected by the fourth quarter of 2024.

Our operations have been financed primarily through our collaborations with AbbVie and GSK and the issuance and sale of convertible preferred stock and of common stock upon the completion of our initial public offering (IPO) and follow-on offering.

To date, we have not had any products approved for sale and have not generated any revenue from product sales. Further, we do not expect to generate revenue from product sales until such time, if ever, that we are able to successfully complete the development and obtain marketing approval for one of our product candidates. We will continue to require additional capital to develop our product candidates and fund operations for the foreseeable future. We have incurred net losses in each year since inception, and we expect to continue to incur net losses for the foreseeable future. Our ability to generate product revenue will depend on the successful development and eventual commercialization of one or more of our product candidates. Our net losses were $45.9 million and $44.6 million for the three months ended March 31, 2023 and 2022, respectively. As of March 31, 2023, we had an accumulated deficit of $625.5 million. Substantially all of our net losses have resulted from costs incurred in connection with our research and development programs and from general and administrative costs associated with our operations. We expect our expenses will increase substantially in connection with our ongoing activities, as we:

advance product candidates through preclinical studies and clinical trials;

pursue regulatory approval of product candidates;

hire additional personnel;

acquire, discover, validate, and develop additional product candidates;

require the manufacture of supplies for our preclinical studies and clinical trials; and

obtain, maintain, expand, and protect our intellectual property portfolio.

On March 28, 2023, we committed to a plan to reduce our workforce by approximately 11% to better align our resources with our previously announced strategic prioritization of our late-stage immuno-neurology programs, including latozinemab in FTD and AL002 and AL101 in AD. We initiated a reduction in force impacting approximately 30 employees across the organization effective March 29, 2023. We expect that our existing cash, cash equivalents and investments will enable us to fund our operating expenses and capital expenditure requirements through 2025, beyond multiple key clinical milestones for our prioritized late-stage programs.

Components of Results of Operations

Revenue

We have not generated any revenue from product sales and do not expect to do so in the near future. Our revenue to date has been primarily related to the AbbVie Agreement and GSK Agreement for the license and co-development of product candidates with those parties. We recognize revenue from the upfront payments and the milestone payment received from AbbVie over time as services are provided. We recognize revenue from the upfront payments from GSK at a point in time for a development license and over time for research and development services. Revenues for research and development services are recognized as the program costs are incurred by measuring actual costs incurred to date compared to the overall total expected costs to satisfy the performance obligation.

Under the terms of our AbbVie Agreement, in addition to receiving the upfront payments from AbbVie, we may also be entitled to development and regulatory milestone payments, opt-in payments for continued development after proof-of-concept for AL002, and other future payments from profit sharing or royalties after commercialization of product candidates from such program. Under the terms of our AbbVie Amendment signed in February 2023, the Company received a $17.8 million milestone payment in March 2023 for the dosing of the first patient in a long-term extension (LTE) trial.

Under the terms of our GSK Agreement, we received $700 million in upfront payments, of which $500 million was received in August 2021 and $200 million was received in January 2022. In addition, we will be eligible to receive up to an additional $1.5 billion in clinical development, regulatory, and commercial launch-related milestone payments for latozinemab and AL101. Alector and GSK are jointly developing latozinemab and AL101.

In the United States, Alector and GSK will equally share profits and losses from commercialization of latozinemab and AL101. We may opt out of the sharing of development costs and of profit and losses from commercialization in the United States on a product-by-product basis. In such case, we will no longer conduct development or commercialization of that product and we will receive royalties on net sales of the product in the United States instead of a share of profits. Outside of



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the United States, GSK will be responsible for commercialization of latozinemab and AL101 for all indications, and we will be eligible for double-digit tiered royalties.

We expect that our revenue for the next several years will be derived primarily from the AbbVie and GSK Agreements. The balance of deferred revenue was $492.9 million as of March 31, 2023, related to the AbbVie and GSK Agreements. The deferred revenue is expected to be recognized over the research and development period of the programs through proof-of-concept for AL002 and the completion of the initial Phase 2 clinical trials for specified indications for latozinemab and AL101.

Research and Development Expenses

Research and development expenses account for a significant portion of our operating expenses. We record research and development expenses as incurred. Research and development expenses consist primarily of costs incurred for the discovery and development of our product candidates, which include:

expenses incurred under agreements with third-party contract organizations, preclinical testing organizations, and consultants;

costs related to production of clinical materials, including fees paid to contract manufacturers;

laboratory and vendor expenses related to the execution of preclinical studies and clinical trials;

personnel-related expenses, including salaries, benefits, and stock-based compensation for personnel engaged in research and development functions;

costs related to the preparation of regulatory submissions;

third-party license fees; and

facilities and other expenses, which include expenses for rent and maintenance of facilities, depreciation and amortization expense, and other supplies.

We expense all research and development costs in the periods in which they are incurred. Costs for certain development activities are recognized based on an evaluation of the progress to completion of specific tasks using information and data provided to us by our vendors, collaborators, and third-party service providers. Nonrefundable advance payments for goods or services to be received in future periods for use in research and development activities are deferred and capitalized. The capitalized amounts are then expensed as the related goods are delivered and as services are performed.

Specific program expenses include expenses associated with the development of our most advanced product candidates: latozinemab, which is being studied in a pivotal Phase 3 clinical trial, INFRONT-3, which has an ongoing Phase 2 clinical trial; AL002, which is being studied in a Phase 2 clinical trial; and AL101, for which we have completed a Phase 1 clinical trial. We also have expenses related to the discovery and development of future product candidates and separately tracked expenses related to programs that we expect to move out of preclinical studies and into Phase 1 clinical trials. These expenses primarily relate to salaries and benefits, stock-based compensation, facility expenses, including depreciation, and lab consumables.

Where we share costs with our collaboration partners, such as in our GSK Agreement, research and development expenses may include cost sharing reimbursements from, or payments to, our partner.

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 expect our research and development expenses to increase substantially for the foreseeable future as we continue to invest in research and development activities related to developing our product candidates, as our product candidates advance into later stages of development, as we begin to conduct larger clinical trials, as we seek regulatory approvals for any product candidates that successfully complete clinical trials, and incur expenses associated with hiring additional personnel to support our research and development efforts. The process of conducting the necessary clinical research to obtain regulatory approval is costly and time-consuming, and the successful development of our product candidates is highly uncertain.

General and Administrative Expenses

General and administrative expenses consist primarily of personnel-related costs, including stock-based compensation, for our personnel in executive, legal, finance and accounting, information technology, human resources, and other administrative functions. General and administrative expenses also include legal fees relating to intellectual property and corporate matters, professional fees paid for accounting, auditing, consulting, and tax services, insurance costs, and facility costs not otherwise included in research and development expenses.



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Other Income, Net

Other income, net consists of interest earned on our cash equivalents and marketable securities and foreign currency transaction gains and losses incurred during the period.

Income Tax Expense

Income tax expense consists of federal and state income tax provisions.

Results of Operations

Comparison of the Three Months Ended March 31, 2023 and 2022



                               Three Months Ended
                                    March 31,             Dollar
                               2023          2022         Change
                                        (In thousands)
Collaboration revenue        $  16,549     $  24,474     $  (7,925 )
Operating expenses:
Research and development        51,887        53,043        (1,156 )
General and administrative      14,777        15,554          (777 )
Total operating expenses        66,664        68,597        (1,933 )
Loss from operations           (50,115 )     (44,123 )      (5,992 )
Other income, net                5,159           264         4,895
Loss before income taxes       (44,956 )     (43,859 )     (10,887 )
Income tax expense                 901           758           143
Net loss                     $ (45,857 )   $ (44,617 )   $ (11,030 )




Revenue

Collaboration revenue was $16.5 million for the three months ended March 31, 2023, compared to $24.5 million for the three months ended March 31, 2022. The decrease was due to less revenue recognized from the GSK Agreement, in particularly for our latozinemab programs, offset by the addition of AL002 LTE revenue. Revenues are recognized as the program costs are incurred by measuring actual costs incurred to date compared to the overall total expected costs to satisfy the performance obligation.

Research and Development Expenses

Research and development expenses were $51.9 million for the three months ended March 31, 2023, compared to $53.0 million for the three months ended March 31, 2022. The decrease of $1.2 million was driven by a $5.3 million decrease in our latozinemab programs due to the timing of manufacturing activities offset by an increase of $4.2 million in the AL002 program due to higher enrollment activities and the addition of the LTE trial.



                                                  Three Months Ended
                                                       March 31,             Dollar
                                                   2023          2022        Change
                                                           (In thousands)
Direct research and development expenses
Latozinemab                                     $    4,311     $  9,653     $ (5,342 )
AL101                                                1,772          650        1,122
AL002                                               11,064        6,822        4,242
Other programs                                       6,974       11,194       (4,220 )
Indirect research and development expenses
Personnel related (including stock-based
  compensation)                                     21,934       18,531        3,403

Facilities and other unallocated research and


  development expenses                               5,832        6,193         (361 )

Total research and development expenses $ 51,887 $ 53,043 $ (1,156 )






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General and Administrative Expenses

General and administrative expenses were $14.8 million for the three months ended March 31, 2023, compared to $15.6 million for the three months ended March 31, 2022. The decrease of $0.8 million was mainly driven by a decrease in consulting expenses related to accounting, recruiting, IT, and other general expenses.

Other Income, Net

Other income, net was $5.2 million for the three months ended March 31, 2023, compared to $0.3 million for the three months ended March 31, 2022. The increase of $4.9 million was due to higher investment yields on our marketable securities.

Income Tax Expense

Income Tax Expense was $0.9 million for the three months ended March 31, 2023, compared to $0.8 million for the three months ended March 31, 2022.

Liquidity and Capital Resources

Since our inception through March 31, 2023, our operations have been financed primarily by our collaborations with AbbVie and GSK and the issuance and sale of convertible preferred stock and of common stock upon the completion of our IPO and follow-on offering.

As of March 31, 2023, we had $669.3 million of cash, cash equivalents, and marketable securities. As of March 31, 2023, we had an accumulated deficit of $625.5 million.

Future Funding Requirements

Our primary uses of cash are to fund our operations, which consist primarily of research and development expenditures related to our programs, and to a lesser extent, general and administrative expenditures. We expect our expenses to continue to increase in connection with our ongoing activities, in particular as we continue to advance our product candidates and our discovery programs. In addition, we expect to incur additional costs associated with operating as a public company.

Based on our current operating plan, we believe that our existing cash, cash equivalents, and marketable securities will enable us to fund our operations and capital expenditure requirements through 2025. We reduced our workforce to better align our resources with our current strategic priorities and maintain our expectations with respect to our ability to fund our operations. We have based this estimate on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect. We may also choose to seek additional financing opportunistically. We may seek to raise capital through public equity or debt financings, license agreements, collaborative agreements or other arrangements with other companies, asset sales, or through other sources of financing. We expect to need to obtain substantial additional funding in the future for our research and development activities and continuing operations. If we were unable to raise capital when needed or on favorable terms, we would be forced to delay, reduce, or eliminate our research and development programs or future commercialization efforts.

Our future capital requirements will depend on many factors, including:

the timing and progress of preclinical and clinical development activities; including, without limitation, our collaboration efforts with AbbVie and GSK;

the number and scope of preclinical and clinical programs we decide to pursue;

successful enrollment in and completion of clinical trials;

our ability to establish agreements with third-party manufacturers for clinical supply for our clinical trials and, if our product candidates are approved, commercial manufacturing;

our ability to maintain our current research and development programs and establish new research and development programs;

addition and retention of key research and development personnel;

our efforts to enhance operational, financial, and information management systems, and hire additional personnel, including personnel to support development of our product candidates;



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the costs associated with workforce reductions;

negotiating favorable terms in any collaboration, licensing, or other arrangements into which we may enter and performing our obligations in such collaborations;

the timing and amount of milestone and other payments we may receive under our collaboration arrangements;

the costs and timing of regulatory approvals;

our eventual commercialization plans for our product candidates;

the effects of inflationary pressures; and

the costs involved in prosecuting, defending, and enforcing patent claims and other intellectual property claims.

A change in the outcome of any of these or other 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. Furthermore, our operating plans may change in the future, and we may need additional funds to meet operational needs and capital requirements associated with such operating plans.

Cash Flows



The following table summarizes our cash flows for the periods indicated (in
thousands):


                                                     Three Months Ended March 31,
                                                       2023                 2022

Cash provided by (used in) operating activities $ (48,548 ) $ 135,091 Cash provided by (used in) investing activities

           88,701              (12,106 )
Cash provided by financing activities                      1,079                2,483


Operating Activities

For the three months ended March 31, 2023, cash used in by operating activities was $48.5 million. This was mainly due to the net loss of $45.9 million. We also had a decrease of $7.0 million in accrued liabilities and accrued clinical supply costs. This was offset by a non-cash charge of $11.0 million for stock-based compensation.

For the three months ended March 31, 2022, cash provided by operating activities was $135.1 million. This was mainly due to the $200 million payment received from GSK. We also had a non-cash charge of $11.9 million for stock-based compensation. This was offset by net loss of $44.6 million and a decrease of $3.4 million in accrued liabilities and accrued clinical supply costs.

Investing Activities

For the three months ended March 31, 2023, cash used in investing activities of $88.7 million was primarily related to the maturities of marketable securities of $210.0 million offset by purchases of marketable securities of $120.3 million.

For the three months ended March 31, 2022, cash used in investing activities of $12.1 million was primarily related to the maturities of marketable securities of $18.7 million offset by purchases of marketable securities of $30.1 million.

Financing Activities

For the three months ended March 31, 2023, cash provided by financing activities of $1.1 million was primarily from the exercise of options to purchase common stock.

For the three months ended March 31, 2022, cash provided by financing activities of $2.5 million was primarily from the exercise of options to purchase common stock.

Critical Accounting Policies and Estimates

Management's discussion and analysis of our financial condition and results of operations is based on our consolidated financial statements, which have been prepared in accordance with generally accepted accounting principles in the United States (GAAP). The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as the reported revenue generated and expenses incurred during the reporting periods. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily



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apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions and any such differences may be material. We believe that the accounting policies discussed below are critical to understanding our historical and future performance, as these policies relate to the more significant areas involving management's judgments and estimates.

Other than the disclosures below, there have been no material changes to our critical accounting policies and estimates from those described in "Management's Discussion and Analysis of Financial Condition and Results of Operations" included in our Annual Report on Form 10-K, as filed with the SEC on February 28, 2023.

Revenue Recognition

We recognize revenue when control of promised goods or services is transferred to customers in an amount that reflects the consideration that is expected to be received for those goods or services. In determining the appropriate amount of revenue to be recognized as we fulfill our obligations under arrangements, we perform the following steps: (i) identify the contract(s) with a customer, (ii) identify the performance obligations in the contract, (iii) determine the transaction price, (iv) allocate the transaction price to the performance obligations in the contract, and (v) recognize revenue when (or as) the entity satisfies the performance obligation. If it is determined that multiple performance obligations exist, the transaction price is allocated at the inception of the agreement to all identified performance obligations based on the relative standalone selling price (SSP). The relative SSP for each deliverable is estimated using external sourced evidence if it is available. If external sourced evidence is not available, we use our best estimate of the SSP for the deliverable.

We recognize collaboration revenue at a point in time if control of the promised good or service has been transferred to the customer. We recognize collaboration revenue over time by measuring the progress toward complete satisfaction of the performance obligation using an input measure. In order to recognize revenue over the research and development period, we measure actual costs incurred to date compared to the overall total expected costs to satisfy the performance obligation. Revenues are recognized as the program costs are incurred. We re-evaluate the estimate of expected costs to satisfy the performance obligation each reporting period and make adjustments for any significant changes. Clinical trials are expensive and can take many years to complete, and the outcome is inherently uncertain. Changes in our forecasted costs are likely to occur over time based upon changes in clinical trial procedures set forth in protocols, changes in estimates of manufacturing costs, or feedback from regulators on the design or operation of our clinical trials. We have had changes to the overall expected costs to satisfy the performance obligations from period to period.

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