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Initial Clinical Data for BEAM -302 in Alpha -1 Antitrypsin Deficiency (AATD) March 10, 2025
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Beam conference call participants Alpha-1 Antitrypsin Deficiency & BEAM-302 Overview Beam’s Vision & Liver Genetic Disease Franchise Introduction Initial BEAM-302 Clinical Data Giuseppe Ciaramella, Ph.D. President John Evans Chief Executive Officer Holly Manning Vice President, Investor Relations & External Communications Amy Simon, M.D. Chief Medical Officer Closing Remarks Mr. Evans Q&A Mr. Evans, Dr. Simon, Dr. Ciaramella & Sravan Emany, Chief Financial Officer TOPIC PARTICIPANT 2
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Cautionary note regarding forward-looking statements This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Such forward-looking statements include statements regarding: the initiation, timing, progress and results of preclinical studies and research and development programs; the initiation, design and progress of clinical trials, including trials for BEAM-101, BEAM-103, BEAM-301 and BEAM-302; the advancement of our pipeline and additional liver programs in multiple preclinical studies; our current expectations and anticipated results of operations, including our expected use of capital; our cash, cash equivalents and marketable securities as of December 31, 2024 and our expectations related thereto; the sufficiency of our capital resources to fund operating expenses and capital expenditure requirements and the period in which such resources are expected to be available; and the therapeutic applications and potential of our technology, including our potential to develop life-long, curative, precision genetic medicines for patients through base editing, including potential safety advantages, all of which are subject to known and unknown important risks, uncertainties and other factors that may cause our actual results, performance or achievements, market trends, or industry results to differ materially from those expressed or implied by such forward-looking statements. Therefore, any statements contained herein that are not statements of historical fact may be forward-looking statements and should be evaluated as such. Without limiting the foregoing, the words "anticipate," "expect," "suggest," "plan," "vision," “strategy,” “possibility,” “promise,” "believe," "intend," "project," "forecast," "estimates," "targets," "projections," "potential," "should," "could," "would," "may," "might," "will," and the negative thereof and similar words and expressions are intended to identify forward-looking statements. Each forward-looking statement is subject to important risks and uncertainties that could cause actual results to differ materially from those expressed or implied in such statement, including, without limitation, risks and uncertainties related to: our ability to develop, obtain regulatory approval for, and commercialize our product candidates, which may take longer or cost more than planned; our ability to raise additional funding, which may not be available; our ability to obtain, maintain and enforce patent and other intellectual property protection for our product candidates; that preclinical testing of our product candidates and preliminary or interim data from preclinical studies and clinical trials may not be predictive of the results or success of ongoing or later clinical trials; that initiation and enrollment of our clinical trials may take longer than expected; that our product candidates or the delivery modalities we rely on to administer them may cause serious adverse events; the uncertainty that our product candidates will receive regulatory approval necessary to initiate or continue human clinical trials; that our product candidates may experience manufacturing or supply interruptions or failures; risks related to competitive products; and the other risks and uncertainties identified under the headings "Risk Factors Summary" and "Risk Factors" and elsewhere in our annual report on Form 10-K for the year ended December 31, 2024, and in any subsequent filings with the Securities and Exchange Commission (the "SEC") which are available on the SEC's website at www.sec.gov. Additional information will be made available by our annual and quarterly reports and other filings that we make from time to time with the SEC. These forward-looking statements speak only as of the date of this presentation. Factors or events that could cause our actual results to differ may emerge from time to time, and it is not possible for us to predict all of them. We undertake no obligation to update any forward-looking statement, whether as a result of new information, future developments or otherwise, except as may be required by applicable law... 3
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OUR VISION IS TO PROVIDE LIFE -LONG CURES for patients suffering from serious diseases POTENTIAL FOR one-time, curative therapies GENE EDITING FOR rare and common diseases PLATFORM FOR rapidly programmable precision medicines 4
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Base editing is an efficient, predictable and potentially best-in-class gene editing technology NUCLEASE CRISPR, ZFN, TALENs Double-stranded breaks Lack of control of gene sequence outcomes Precision targeting with CRISPR …A C G - - - - G C A T… …A C G T C G C T T A T G C A T… …A - - - - - T G C A T… …A C G T C T A T G C A T… …A C - - - - - - - A T… …A C G T C A A C - - G C A T… Etc. - - - - - Deletions A G C T Insertions Enzymatic base conversion Highly efficient, with predictable gene sequence outcomes Precision targeting with CRISPR BASE EDITING BEAM THERAPEUTICS 5
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Key elements of Beam’s leadership position in gene editing BASE EDITING PLATFORM Clinical Validation, Fully Integrated Manufacturing MULTIPLE CATALYSTS Expected in 2025 RAPID EXECUTION for Clinical Programs HIGH VALUE FRANCHISES with Best-in-Class Potential With proceeds from today’s $500M financing, along with $850.7M in cash, cash equivalents and marketable securities as of December 31, 2024, our anticipated cash runway extends into 2028 6
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Strategic focus areas with potential for significant value creation and patient impact HIGH VALUE FRANCHISES with Best-in-Class Potential • Best-in-class potential for BEAM- 101 in sickle cell disease (SCD) → Initial data at ASH 2024 • Well established FDA path to BLA • Lifecycle strategy with ESCAPE and in vivo editing • Platform for future hematology pipeline Hematology • Best-in-class potential for BEAM- 302 in alpha-1 antitrypsin deficiency (AATD) → Initial data today • Potential one-time treatment for AATD lung and liver manifestations under normal gene regulation • Platform for future liver-targeted pipeline Liver Genetic Diseases 7
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BEAM-302 initial clinical data provide proof-of-concept as a potential treatment for AATD and for in vivo base editing broadly HIGH VALUE FRANCHISES with Best-in-Class Potential LIVER GENETIC DISEASES • Well tolerated at all dose levels • Increased total AAT above therapeutic threshold at third dose level • Significantly increased circulating corrected M-AAT and decreased mutant Z-AAT in dose dependent manner • Newly produced AAT in circulation (canonical M and M-variant) functional at neutrophil elastase inhibition • First proof-of-concept for in vivo gene correction with base editing • First Beam in vivo data in liver • Demonstration of Beam’s state- of-the-art lipid nanoparticle (LNP) and in-house manufacturing capabilities • Foundation for platform for future liver-targeted pipeline BEAM-302 FRANCHISE CONFIDENTIAL 8
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What if we could use base editing to correct disease-causing mutations in vivo? 9
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Alpha-1 antitrypsin deficiency (AATD) is a genetic disorder that leads to lung and liver disease Normal AAT Function Genetics Liver Lung AAT Deficiency Wild type SERPINA1 gene (PiM or “M” allele) M-AAT protein is secreted from liver E342K mutation (PiZ or “Z” mutation) Z-AAT aggregates and causes liver damage Decreased AAT secretion plus circulating Z-AAT aggregates lead to lung damage M-AAT protein protects lungs from inflammatory mediators (i.e., elastases) ~30% patients have liver disease, including fibrosis and cirrhosis PiZZ genotype is >95% of severe AATD population >100,000 PiZZ individuals in the U.S.; ~10% are diagnosed ~80% patients have lung disease, including early onset emphysema, chronic cough, shortness of breath Clark et al, Journal of Hepatology 2018; vol 69:1357-1364; Stoller JK, Hupertz V, Aboussouan LS. Alpha-1 Antitrypsin Deficiency. 2006 Oct 27 10
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• Increase circulating total AAT above 11µM “protective threshold” – No severely deficient individuals (PiZZ) have AAT > 11µM – Clinically accepted level for augmentation approval, which demonstrated some clinical benefit – Development of lung or liver disease in individuals with ≥ 1 abnormal AAT alleles requires exposure to additional risk factors (e.g., smoking, obesity) • Reduce Z-AAT levels in the liver and blood to prevent ongoing organ damage • Restore physiologic control of AAT during periods of inflammation to minimize lung damage Increasing total AAT levels above protective threshold reduces patients’ lifetime risks for lung and/or liver disease Micromolar (µM) Adapted from Franciosi et al, ERJ 2022 and from Vidal et al, Arch Bronconeumol 2006; Brode et al, CMAJ 2012 No Disease No Disease Unless Other Risk Factor Present Disease Genotype MM MZ SZ ZZ AAT < 11µM 0% 0% ~40% 100% Emphysema risk No Very Low Low High Liver disease risk No Possibly Possibly High Critical Attributes for an AATD TherapeuticAAT Levels and Disease Manifestations Across Genotypes 11
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AATD current management and unmet needs • Routine emphysema care: bronchodilators, inhaled steroids, oxygen and antibiotics, as needed • Only approved therapy: plasma-derived AAT (augmentation therapy) given intravenously weekly - Does not reduce mutant Z-AAT protein in the liver - Unable to increase AAT levels during inflammation - Slows progression of lung disease, but does not prevent ongoing lung damage and destruction • No approved therapies for liver disease currently • Supportive care • Liver transplantation for late-stage liver disease • RNAi therapies in late-stage development, but do not treat lung manifestations Lung disease treatment Liver disease treatment McElvaney, et al, Expert Review of Respiratory Medicine 2023, 17:3, 191-202; Sandhaus, et al, Chronic Obstr Pulm Dis. 2016 Jun 6;3(3):668-68 12
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BEAM-302 is a potential one-time therapy that uses base editing to directly correct the E342K mutation causing AATD CRISPR Protein Deaminase Guide RNA Corrected SERPINA1 gene PiM E342K mutation PiZ BEAM-302 BASE EDITOR 13
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Advantages of LNP delivery Beam has also established leading LNP capabilities for in vivo treatment of liver-targeted genetic diseases ✓ Outpatient dosing via simple IV infusion ✓ Titratable and redosable ✓ Synthetic and highly scalable manufacturing process ✓ Once optimized, potential for predictable and reproducible platform ✓ Low cost of goods Beam's LNP Leadership Position • Significant investment and expertise in LNP optimization and process development • Internal and externally sourced ionizable lipids • Internal GMP capabilities in NC facility to manufacture at scale • Beam LNPs have shown high levels of tolerability and potency in preclinical studies • Re-usable platform for future liver programs – changing base editor target not expected to change LNP tolerability or efficacy • Actively exploring potential to retarget LNPs to other tissues (e.g., HSCs) PEG Lipid Ionizable Lipid Structural Lipid Sterol Base Editor mRNA Guide RNA GMP = good manufacturing practice; HSCs = hemopoietic stem cells 14
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BEAM-302 has the potential to be the only one-time treatment for both lung and liver manifestations of AATD Correct DNA mutation – the root cause of disease Increase secreted AAT to prevent lung damage Decrease mutant Z-AAT to prevent liver damage Restore physiologic control of AAT during inflammation Durable, one- time treatment, without chronic administration BEAM-302 has potential to address critical aspects of AATD 15
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Vehicle 0.05mpk 0.1mpk 0.25mpk 0.5mpk 0.75mpk 1mpk 2mpk 0 50 100 150 %Serum AAT isoform Corrected AAT PiZ AAT In preclinical in vivo studies, BEAM-302 resulted in both increased serum total & corrected M-AAT and decreased mutant Z-AAT 0 20 40 60 0 20 40 60 80 0 20 40 60 80 Editing efficiency (%) Total AAT (μM) PiZ AAT (μM) Serum AAT (LC-MS) NSG-PiZ Mouse Presented at Alpha-1 Antitrypsin Deficiency 2023 Meeting Corrected M-AAT Mutant Z-AAT 16
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Initial BEAM-302 Clinical Data 17
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Phase 1/2 trial of BEAM-302 designed to achieve clinical proof of concept in patients across the spectrum of AATD • First ever clinical proof-of- concept of in vivo base editing leading to correction of a disease-causing mutation • CTA clearances achieved in four countries • Global site activation and enrollment ongoing Part A: AATD-associated Lung Disease Part B: AATD-associated Liver Disease with or without Lung Disease Assess early safety and efficacy and identify optimal dose for pivotal study • Up to 4 dose cohorts • Patients included with mild to moderate liver disease • Up to 4 dose cohorts • Patients excluded with liver disease Dose Exploration Dose Expansion Dose Exploration Dose Expansion 18
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Initial clinical data includes nine patients across first three dose cohorts 19 Part A: AATD-associated Lung Disease Part B: AATD-associated Liver Disease with or without Lung Disease • Up to 4 dose cohorts • Patients included with mild to moderate liver disease Dose Exploration Dose Expansion Dose Exploration Dose Expansion DOSING COMPLETE in first 3 cohorts of Part A Cohort 3 60 mg N = 3 Cohort 2 30 mg N = 3 Cohort 1 15 mg N = 3 Cohort 4 • 18-70 years of age • Homozygous for PiZZ mutation • Blood total AAT level < 11µM • FEV1 > 40% predicted; FEV/FVC < 70% • Confirmed diagnosis of emphysema • No evidence of liver disease PART A: KEY ELIGIBILITY CRITERIA • Phase 1: Safety and efficacy (AAT, corrected M-AAT, functional AAT, Z-AAT) of BEAM-302 • Phase 2: Efficacy and Safety of BEAM-302; confirm optimal biologic dose PART A: KEY OBJECTIVES & ENDPOINTS
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Patient demographics PATIENT DEMOGRAPHICS 15 mg (N=3) 30 mg (N=3) 60 mg (N=3) Gender, n Male 2 2 3 Female 1 1 0 Age in years, median (min, max) 49 (37, 53) 58 (53, 61) 48 (38, 57) Weight (kg), median (min, max) 92.4 (76.0, 93.1) 72.2 (71.7, 83.0) 88.1 (76.5, 98.5) Baseline FEV1 % predicted, mean (SE) 57.7 (6.96) 61.2 (4.31) 58.7 (11.09) Baseline total AAT levels (µM), mean (SE) 4.4 (0.22) 5.3 (0.25) 4.4 (0.30) Years since AATD diagnosis [1], median (min, max) 3.0 (2.4, 14.4) 10.1 (1.5, 17.6) 3.9 (1.7, 4.4) [1] Calculated as (date of informed consent signed – date of AATD diagnosis +1)/365.25. Partial diagnosis dates are imputed as 01 of the Month if the Day is missing or 01 January of the year if both Month and Day are missing. For total AAT, baseline for each patient is defined as the average of all assessments conducted within the 84-day screening period prior to BEAM-302 infusion. For other variables, baseline is defined as the last available assessment prior to BEAM-302 infusion. 20
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Preliminary data support the safety of BEAM-302 at doses up to 60 mg Data cutoff February 26, 2025 Data are based on follow-up exposure data between approximately 28 days and 8 months Related events include events where investigator has assessed relationship as possibly or definitely related to BEAM-302 Related events include 2 patients at the 15mg dose each with 1 IRR (mild); 1 patient at the 60mg dose with IRR (mild) and back pain (moderate) Patients with 15 mg N=3 n (%) 30 mg N=3 n (%) 60 mg N=3 n (%) Any TEAEs 3 (100) 3 (100) 2 (66.7) Related to BEAM-302 2 (66.7) 0 1 (33.3) Any TEAEs ≥Grade 3 0 0 0 Dose-limiting toxicities 0 0 0 Serious TEAEs 0 0 0 Death 0 0 0 • No serious AEs, DLTs or ≥Grade 3 AEs observed • All treatment-emergent AEs (TEAEs) were mild-to-moderate • Grade 1 asymptomatic elevations in ALT (+/- AST) were observed within the first 28 days after dosing in all cohorts • 3 patients had mild infusion-related reactions (IRR) that resolved without intervention or interruption (2 at 15 mg; 1 at 60 mg) • Most common AEs occurring in ≥ 2 patients included: upper respiratory tract infection, back pain, IRR and infective exacerbation of chronic obstructive airways disease 21
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N = 3 3 3 3 3 3 3 3 3 7 3 3 3 14 3 3 2 21 28 Days since BEAM-302 infusion 0 50 100 150 200 ALT (U/L) Grade 2 Grade 1 3 3 3 0 50 100 150 200 AST (U/L, Mean ± SD) Grade 1 Grade 2 Asymptomatic, Grade 1 liver transaminase elevations were observed in some patients following BEAM-302 treatment Data cutoff February 26, 2025 Grade 1 is defined as: > upper limit of normal (ULN) - 3.0 x ULN if baseline was normal; 1.5 - 3.0 x baseline if baseline was abnormal; ULN is calculated using a weighted average of male and female reference values, based on the proportion of each gender in the study. One patient in the 15 mg cohort could not attend their Day 21 visit due to a COVID infection. Bilirubin levels remained within the normal range or at baseline across all dose cohorts ALT (U/L, Mean ± SD) 3 3 3 1 3 3 3 2 3 3 3 7 3 3 3 14 3 3 2 21 3 3 3 28 Days since BEAM-302 infusion 3 2 2 1 3 2 3 3 3 3 3 2 15 mg 30 mg 60 mg 15 mg 30 mg 60 mg N = 3 2 3 3 22
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0 2 4 6 8 10 12 14 16 BEAM-302 treatment led to a rapid, dose-responsive increase of total AAT above the 11µM protective threshold Data cutoff February 26, 2025 Baseline for each patient is defined as the average of all assessments conducted within the 84-day screening period prior to BEAM-302 infusion. One patient in the 15 mg cohort could not attend their Day 21 visit due to a COVID infection. Serum Concentration (μM) 15 mg 30 mg 60 mg Total AAT by Turbidimetry (Mean ± SE) Dose Baseline, mean Total AAT at Day 28, mean 15 mg 4.4µM 7.0µM 30 mg 5.3µM 10.1µM 60 mg 4.4µM 12.4µM Visit 3 3 3 3 3 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 N = Protective threshold 23
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0 0.5 1 1.5 2 2.5 3 Dose-dependent increase in fold change in total AAT observed following treatment with BEAM-302 Data cutoff February 26, 2025 Baseline for each patient is defined as the average of all assessments conducted within the 84-day screening period prior to BEAM-302 infusion. One patient in the 15 mg cohort could not attend their Day 21 visit due to a COVID infection. N = Fold Change in Total AAT by Turbidimetry (Mean ± SE) Fold Change Over Baseline 15 mg 30 mg 60 mg Dose Baseline, mean Fold Change in Total AAT at Day 28, mean 15 mg 4.4µM 1.6x 30 mg 5.3µM 1.9x 60 mg 4.4µM 2.8x Visit 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 3 3 3 3 3 3 24
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60 mg30 mg15 mg 0 10 20 30 40 50 60 70 80 90 100 Proportion (%) Corrected M-AAT was detected in the circulation of patients for the first time within 3 days after BEAM-302 treatment Proportion (%) of Corrected M-AAT and Mutant Z-AAT by LC-MS by Cohort (Mean ± SE) Data cutoff February 26, 2025 Baseline for each patient is defined as the average of all assessments conducted within the 84-day screening period prior to BEAM-302 infusion. One patient in the 15 mg cohort could not attend their Day 21 visit due to a COVID infection. Donato et al. Respiratory Research (2015) 16:96 Mutant Z-AATCorrected M-AAT 0% 0% 2% 24% 38% 39% 45% 46% 48% 47% 55% 56% N = 3 3 3 3 3 2 3 3 3 3 1 1 3 3 3 3 13 3 3 3 3 3 3 3 0% 0% 5% 31% 52% 58% 60% 63% 0% 2% 15% 68% 88% MZ genotype profile: 80% M, 20% Z in circulation 25 Visit
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-120 -100 -80 -60 -40 -20 0 20 BEAM-302 treatment also led to rapid, dose-dependent reductions in circulating mutant Z-AAT Data cutoff February 26, 2025 Baseline for each patient is defined as the average of all assessments conducted within the 84-day screening period prior to BEAM-302 infusion. One patient in the 15 mg cohort could not attend their Day 21 visit due to a COVID infection. % Change Mutant Z-AAT from Baseline by LC-MS (Mean ± SE) N = 3 3 3 Visit Percent Change from Baseline (%) 60 mg 30 mg 15 mg Dose % change in Z-AAT at Day 28, mean 15 mg -11% 30 mg -38% 60 mg -78% 3 3 3 3 3 3 3 3 3 3 3 3 2 3 3 3 1 26
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Data cutoff February 26, 2025 AAT correction was durable, with up to 6 months of follow-up, after a single dose of BEAM-302 Patient baseline defined as the average of all assessments conducted within the 84-day screening period prior to BEAM-302 infusion. Durability of Total AAT, Corrected M-AAT and Mutant Z-AAT by LC-MS Beyond Month 1 (Mean ± SE) Total AAT (LC-MS)Mutant Z-AATCorrected M-AAT Visit 30 mg15 mg 0 3 6 9 12 15 18 Serum Concentration (μM) 3 3 3 3 3 3 3 33 3 3 3 3 2 3 3 3 3 1 1 N = N = 27
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0 3 6 9 12 15 18 N = Increased total AAT in circulation was functional in neutrophil elastase inhibition assay Baseline for each patient is defined as the average of all assessments conducted within the 84-day screening period prior to BEAM-302 infusion. Total AAT (Turbidimetry) and Functional AAT (Inhibition) by Cohort (Mean ± SE) Increased total AAT in circulation also functional in neutrophil elastase binding assay Total AAT (Turbidimetry)Functional AAT (Inhibition) Visit 30 mg15 mg Serum Concentration (µM) N = Data cutoff February 26, 2025 3 3 3 3 3 3 3 3 3 3 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 60 mg 3 3 3 3 3 3 3 3 3 3 1 3 1 3 N = CONFIDENTIAL 28
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Established clinical proof of concept for BEAM-302 as a potential one-time, differentiated treatment for AATD To date, BEAM-302 was well tolerated with an acceptable safety profile at 15, 30, 60 mg doses • All adverse events (AEs) were mild to moderate, with no serious AEsand no dose-limiting toxicities (DLTs) • Asymptomatic Grade 1 ALT and AST elevations and transient Grade 1 infusion-related reactions were observed in some patients and have not required treatment Single dose of BEAM-302 led to durable, dose-dependent correction of the PiZ mutation • Demonstrated by increases in total AAT, production of corrected M-AAT, and decreasedmutant Z-AAT in circulation Total AAT increased to a mean of 12.4µM for patients treated with the60 mg dose (N=3) • Above the protective threshold of 11µM Mutant Z-AAT reduced up to 78% in circulation in a dose-dependent manner • M-AAT to Z-AAT ratio above 80% in circulation, similar to the MZ genotype Increased total AAT is functional by both neutrophil elastase inhibition and neutrophil elastase binding assays 29
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Anticipated next steps in development of BEAM-302 for AATD Part A: AATD-associated Lung Disease Part B: AATD-associated Liver Disease with or without Lung Disease • Up to 4 dose cohorts • Patients included with mild to moderate liver disease • Up to 4 dose cohorts • Patients excluded with liver disease Dose Exploration Dose Expansion Dose Exploration Dose Expansion 30 • Continue dose escalation to identify optimal biologic dose • Expand country and site activation, including U.S. • Present updated data in 2H 2025 • Initiate dose exploration in 2H 2025
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Wrap up 31
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BEAM-302 has the potential to be the only one-time treatment for both lung and liver manifestations of AATD Correct DNA mutation – the root cause of disease Increase secreted AAT to prevent lung damage Decrease mutant Z-AAT to prevent liver damage Restore physiologic control of AAT during inflammation Durable, one- time treatment, without chronic administration BEAM-302 has potential to address critical aspects of AATD 32
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Broader implications of BEAM-302 dataset Base editing delivers first ever genetic correction of a disease- causing mutation in DNA Proprietary, well- tolerated LNP creates a strategic platform for future liver programs 3 of 3 Beam base editing programs have delivered clinical proof of concept in line with preclinical studies Milestone event in genetic medicine Validation of Beam in vivo LNP capabilities Beam track record of clinical translation 33
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Significant potential catalysts on the horizon BEAM-101 SCD (BEACON TRIAL) • Dose 30 patients by mid-2025 • Dose and continue to enroll adolescent patients • Present updated data in mid-2025 BEAM-302 AATD ✓ Present initial data from multiple cohorts in 1H 2025 • Complete Part A dose escalation and initiate Part B dose escalation • Present updated data in 2H25 ESCAPE SCD & BETA-THALASSEMIA • Initiate Phase 1 healthy volunteer trial of BEAM-103 antibody by YE BEAM-301 GSD1a • Dose first patient in Phase 1/2 trial in early 2025 MULTIPLE CATALYSTS Expected in 2025 34
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Kyle SICKLE CELL DISEASE Dan and Kathi ALPHA-1 ANTITRYPSIN DEFICIENCY Alyssa and Gayle GLYCOGEN STORAGE DISEASE 1A Patients are at the heart of our vision 35