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Corporate Presentation November 2025
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Disclaimers and forward-looking statements This presentation and the accompanying discussion contain forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, including, but not limited to, express or implied statements regarding the Company’s plans, progress, and timing relating to the Company’s clinical programs and the presentation of data, the Company’s current and future research and development plans or expectations, the structure, timing and success of the Company’s planned preclinical development, submission of INDs, and clinical trials, the potential benefits of any of the Company’s prop rietary platforms or current or future product candidates in treating patients, the Company's ability to fund its operating expenses and capital expenditure require ments with its existing cash and cash equivalents, and the Company’s goals and strategy. TScan intends such forward-looking statements to be covered by the safe harbor provisions for forward-looking statements contained in Section 21E of the Securities Exchange Act of 1934 and the Private Securities Litigation Reform Act o f 1995. In some cases, you can identify forward-looking statements by terms such as, but not limited to, “may,” “might,” “will,” “objective,” “intend,” “should,” “could,” “can,” “would,” “expect,” “believe,” “anticipate,” “project,” “target,” “design,” “estimate,” “predict,” “potential,” “plan,” “on track,” or similar expressions or the negative of those terms. Such forward- looking statements are based upon current expectations that involve risks, changes in circumstances, assumptions, and uncerta inties. The express or implied forward-looking statements included in this presentation are only predictions and are subject to a number of risks, uncertaintie s and assumptions, including, without limitation: the beneficial characteristics, safety, efficacy, therapeutic effects and potential advantages of TScan’s TCR-T therapy candidates; TScan’s expectations regarding its preclinical studies being predictive of clinical trial results; the timing of the initiation, prog ress and expected results of TScan’s preclinical studies, clinical trials and its research and development programs; TScan’s plans relating to developing and commercializing its TCR-T therapy candidates, if approved, including sales strategy; estimates of the size of the addressable market for TScan’s TCR-T therapy candidates; TScan’s manufacturing capabilities and the scalable nature of its manufacturing process; TScan’s estimates regarding expenses, future milestone payments and revenue, capital requirements and needs for additional financing; TScan’s expectations regarding competition; TScan’s anticipated growth strategies; TScan’s ability to attract or retain key personnel; TScan’s ability to establish and maintain development partnerships and collaborations; TScan’s expectations regarding federal, state and foreign regulatory requirements; TScan’s ability to obtain and maintain intellectual property protection for its proprietary platform technology and our product candidates; the sufficiency of TScan’s existing capital resources to fund its future operating expenses and capital expenditure requirements; and other factors that are described in the “Risk Factors” and “Management’s Discussion and Analysis of Financial Condition and Results of Operations” sections of TScan’s most recent Annual Report on Form 10-K and any other filings that TScan has made or may make with the SEC in the future. Any forward-looking statements contained in this presentation represent TScan’s views only as of the date hereof and should not be relied upon as representing its views as of any subsequent date. Except as requi red by law, TScan explicitly disclaims any obligation to update any forward-looking statements. 2
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TScan is a fully integrated, next-generation TCR-T cell therapy company 3 HEME MALIGNANCY PROGRAM • Targets residual disease to prevent relapse in patients undergoing bone marrow transplant • Promising data: 14 of 17 (82%) of subjects who received TSC-101 remain relapse-free as compared to 9/14 (64%) control-arm subjects(1) • Launch of pivotal study expected in Q2 2026 • Substantial commercial opportunity, with potential to expand addressable market with additional INDs to be filed in 4Q25 SOLID TUMOR PROGRAM • First patients dosed with multiplex TCR-T therapy on the PLEXI-T study with initial safety and efficacy data expected in 1Q26 • With our target discovery platform and ex vivo clinical experience, we are uniquely positioned to develop in vivo-engineered multiplex TCR-T for solid tumors • Working with strategic partner to develop “off-the-shelf” in vivo- engineered TCR-T cell therapy Discovery AUTOIMMUNITY PROGRAM • TScan’s proprietary platform enables the discovery of disease-driving autoantigens in areas of high unmet medical need • Targets identified for systemic sclerosis, ulcerative colitis, ankylosing spondylitis, and birdshot uveitis(2) • Ongoing collaboration with Amgen for target discovery in Crohn’s disease (1) As of latest data cut of July 18, 2025; Al-Malki et al, abstract ID 2391 to be presented at ASH Annual Meeting December 2025; IND: investigational new drug; (2) Weinheimer et al, and Pryor et al, presented at ACR Convergence 2025, abstracts 0888, 0997 (3) Includes 56,747,993 outstanding common shares plus 73,087,945 pre-funded warrants Clinical Preclinical $184.5M as of Sept 30, 2025 funds operations into H2 2027 129.8M(3) total economic shares outstanding as of Sept 30, 2025
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Promising pipeline across multiple therapeutic areas 4 HLA typeIndications Targets HLA-A*02:01 HLA-A*02:01 HLA-B*07:02 HLA-A*02:01 HLA-A*01:01 TSC-101 (HA-2) HEMATOLOGIC MALIGNANCIES SOLID TUMORS AML, MDS NSCLC, Sarcoma, Head & Neck, Cervical, Anal & Genital AUTOIMMUNITY IND-enabling Phase 1 Pivotal HLA-A*03:01 ALLOHATM PLEXI-TTM Target-directed therapeutics Engineered TCR-T cell therapies Pivotal launch Q2 2026 Crohn's Systemic sclerosis Ulcerative colitis Ankylosing spondylitis Birdshot uveitis TSC-102 (CD45) HPV16 MAGE-C2 MAGE-A4 PRAME MAGE-A1 Discovery/Preclinical In vivo-engineered TCR-Ts HLA-A*01:01 HLA-A*24:02
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Executed on milestones in 2025, momentum continues into 2026 5 Aligned on final pivotal design for TSC-101 Two-year relapse data from initial TSC-101 patients Heme Program File two INDs for TSC-102 (A*03:01 and A*01:01) Opened expansion cohorts at DL3 Auto- immunity Identified novel autoantigens Presented preclinical data for lead programs Safety and response data from PLEXI-T trial in Q1 Solid Tumor Program First patients treated with multiplex TCR-T therapy Dose escalation completed for singleplex TCR-T tx Launch pivotal trial for TSC-101 in Q2 H2 2025 2026H1 2025 Proof-of-concept for therapeutic approach
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Heme Malignancies: Targeting residual disease to prevent relapse in patients undergoing allogeneic HCT
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TScan is working to treat residual disease and prevent relapse in heme malignancies 7 Current Standard of Care Unmet Medical Need TScan Approach Allogeneic hematopoietic cell transplant (Allo-HCT) is the only potential cure for patients with AML and MDS 38-44% of patients relapse within two years following Allo-HCT with reduced intensity conditioning (RIC)* TCR-T cell therapy targeting antigens on patient cells, but not donor cells, to prevent relapse after transplant TSC-101 is a TCR-T cell therapy designed to eliminate residual cancer and prevent relapse following Allo-HCT in HLA-A*02:01- positive patients * CIBMTR analysis of AML, ALL, MDS allogeneic transplants with reduced intensity conditioning (RIC) between 2017- 2019 with 2-year follow-up;
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TSC-101 is a TCR-T cell therapy designed to eliminate residual cancer and prevent relapse following Allo-HCT 8 TSC-101 PATIENT (HLA-A*02:01-positive) TSC-101 DONOR (HLA-A*02-negative) Hematopoietic cell transplant Cancer cell Normal blood cell Stem cell T cell HA-2 positive HA-2 negative HA-2 negative HA-2 positive TSC-101 Residual cancer Stem cells TCR-T cell infusion TCR-T manufacturing T-cell HA-2 TCR
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Relapse following allogeneic HCT highlights a key unmet medical need 9 Patients diagnosed with AML & MDS ~9K allogeneic HCTs conducted annually in the U.S.* Many patients respond to treatment and remain in remission Patients who relapse following SOC transplant, however, have high associated mortality, creating an unmet medical need Our goal is to eliminate residual cancer using TCR-T cell therapy to prevent relapse after transplant Allo-HCT eliminates a patient’s blood cells, including their malignant cells, and replaces them with new healthy blood cells from the donor * Source: CIBMTR, SEER, 2024 Transplant + TSC-101 TCR-T cell therapy Patients diagnosed with AML & MDS Patients respond and remain in long-term remission Transplant T
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ALLOHA , a multi-arm Phase 1 trial for TSC-101 in subjects with AML, ALL, and MDS (NCT05473910) 10 HCTPre-transplant screening Endpoint and safety monitoringRIC Day 0 Day +21 Day +61 Donor screening Manufacturing apheresis HCT apheresis TSC-101 Infusion 1 TSC-101 Infusion 2 Subject screening Control Arm Transplant alone Treatment Arm Transplant + TSC-101 Key eligibility criteria • Age >18 years • Undergoing first allo-HCT for ALL, AML, MDS • Subject positive for HA-2 with a haploidentical HA-2 negative donor • Eligible for RIC-HCT followed by PTCy for GvHD prophylaxis Key endpoints • Safety: Dose limiting toxicities, adverse events • Efficacy • Exploratory endpoints: Donor chimerism, minimal residual disease ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; MDS, myelodysplastic syndromes; GvHD, graft vs host disease; RIC-HCT, reduced intensity conditioning hematopoietic cell transplantation
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TSC-101 delivers a predictable, easily planned treatment journey 11 Patient enrollment Day 0 HCT transplant Donor apheresis 1: T-cells Donor apheresis 2: Stem cells Day 21 Infusion 1 Day 61 Infusion 2 Follow up TSC-101 Manufacturing, Release & Shipment Day -10 to -1 Reduced Intensity Conditioning Discharge, Post- treatment monitoring & follow up Stem cellsT cells Infusion 1 & 2 site of care (inpatient vs outpatient) determined by administering physician. Infusion 1 may be given upon engraftment and between days 14-35 post transplant, infusion 2 would be administered about 40 days after infusion 1. * *
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Compelling data presented at 66th Annual ASH Meeting in 2024 12 Al-Malki et al, presented at ASH Annual Meeting 2024
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Recently updated ALLOHA Phase 1 data support launch of pivotal trial in Q2 2026 13 Infusions with TSC-101 were well-tolerated with no DLTs and adverse events following HCT + TSC-101 were consistent with HCT alone TSC-101 TCR-T cells have been detected >2 years post infusion and have a clear dose-persistence relationship 14 of 17 (82%) treatment-arm subjects remain relapse-free as compared to 9/14 (64%) control-arm subjects* Attractive safety profile Long-term persistence Meaningful relapse-free benefit * Al-Malki et al, abstract ID 2391, ASH Annual Meeting December 2025
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Pivotal trial design for TSC-101 uses a biologically-assigned control arm to support relapse-free survival as the primary endpoint 14 Biological assignment • Company has reached agreement with the FDA to use a pivotal trial design that mirrors the ALLOHA Phase 1 trial (NCT05473910) • All patients that are eligible for TSC-101 will be assigned to the investigational arm Two infusions of TSC-101 RIC-based transplant Follow up Study Population • AML or MDS • Age > 18 years • Undergoing first allo-HCT • Eligible for reduced intensity conditioning (RIC) Key Endpoints • Primary Endpoint: RFS • Key Secondary Endpoint: OS AML: Acute myeloid leukemia; MDS: Myelodysplastic syndromes; Allo-HCT: Allogeneic hematopoietic cell transplantation; RIC: Reduced intensity conditioning; RFS: Relapse-free survival; OS: Overall survival Investigational Arm A*02:01-positive subject with A*02-negative donor Control Arm A*02:01-negative subject or A*02:01-positive subject with no available mismatched donor
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Heme Development Strategy Targeting residual disease to prevent relapse in patients undergoing allogeneic HCT
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• TCR-T cells engineered from healthy donor T cells, resulting in more consistent product • Allogeneic therapy allows for manufacturing to be completed prior to ideal infusion time • Global CDMO engaged for scaled up manufacturing; initial tech transfer completed • TSC-101 is used with current SOC transplant; limited practice change required • Transplantation occurs in concentrated treatment centers, simplifying patient identification • HLA-defined patient eligibility through standard testing TSC-101 is a first-in-class TCR-T cell therapy with an exciting commercial opportunity 16 Streamlined Commercial Operations Commercial-Ready Manufacturing Strong Value Proposition: TSC-101 has positive early efficacy & safety data, addressing a major unmet need in the post-transplant setting where no therapeutic agents are approved Sources: Simon Kucher pricing analysis • Favorable pricing corridor established in the range of recent cell therapy approvals • Clear reimbursement pathway being mapped with payers • Established patient access strategy to enable rapid uptake of TSC-101 Market Access Planning Underway
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AML ALL -2 0 2 4 6 8 10log2(TPM+0.001) Source: TCGA • CD45 is a lineage-specific antigen with expression in all hematopoietic cells, including HSCs • CD45 is a large protein with many well-known epitopes for high frequency HLAs • Antigen-negative donors can be selected by mismatching on HLA (using haploidentical and MMUD donors) TCRs for additional HLA types will target epitopes on CD45, a universal source of antigens for heme malignancies 17 HA-1 HA-1HA-2 HA-2 CD45CD45 TSC-102-A0301 targets an antigen from CD45 presented on HLA-A*03:01 0 20 40 60 80 0 50 100 200400600800 U937 E:T of 5:1 Time (hour) Cell Survival (%) TSC-102-A0301 Non-engineered T cells E:T of 5:1 U937 (Myeloid leukemia) CD45 has high and uniform expression in AML and ALL Data on file
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A*02:01 A*03:01 A*01:01 A*24:02 HLA Total 42% 22% 24% 17% ~78% 47% 25% 26% 19% ~83% 19% 7% 14% 37% ~50% Current TSC- 101 Program INDs Planned for 2025 Discovery/ Preclinical TScan is targeting the most frequent human leukocyte antigens (HLAs) to address a broad patient population 18 Sources: Allelefrequencies.net; Note: Patients can be positive for multiple HLA types. U.S. EU APAC HLA Expression: Addition of HLA-A*03:01 and HLA-A*01:01 products expands U.S. and EU markets Addition of an HLA-A*24:02 program unlocks broader APAC market TSC-101 targets ~45% of US and EU populations
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Expansion opportunities for the program provide a way to reach over 20,000 patients in North America, Europe, and APAC 19 Capturing an expanding treatment landscape: Expansion driven by launch of products for additional HLA types.* Plan to file INDs for TSC-102-A0301 and TSC-102-A0101 by YE2025 Additional patient populations (e.g., relapse refractory patients, other indications) may become addressable with a proven safe and effective relapse prevention strategy0 5,000 10,000 15,000 20,000 25,000 TSC-101 HLA expansion Transplant + Disease expansion # of addressable patients (global) Source: SEER, CIBMTR, EBMT, APBMT, ClearView analysis * Additional HLA types include A*03:01, A*01:01, and A*24:02
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20TScan Therapeutics, Inc. Heme Program Progress and Anticipated Milestones Reached agreement with FDA on pivotal trial design Transferred commercial manufacturing process to external CDMO File INDs for TSC-102-A0301 and TSC-102-A0101 YE 2025 Launch pivotal study for TSC-101 in Q2 2026 Two-year relapse data from initial TSC-101 patients Dec 2025
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Solid Tumors Developing multiplex TCR-T therapy to overcome tumor heterogeneity
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TScan is developing multiplex TCR-T cell therapy for solid tumors 22 Solid tumors remain difficult to treat and cure, representing a large unmet medical need Only 10-35%* of patients diagnosed with metastatic solid tumors survive more than 5 years Tumors are heterogeneous – Not every cancer cell expresses a given target, making it difficult to address the whole tumor with a single agent Single agents drive initial responses, but remaining cancer cells eventually expand to drive relapse TScan’s TCR-Ts are designed to be used in combination to overcome tumor heterogeneity, eliciting deep and durable responses In vivo engineering platform currently being developed to enable off-the-shelf multiplex TCR-T cell therapy Unmet Medical Need Challenges in Treating Solid Tumors TScan’s Solution Source: SEER * Across HNSCC, NSCLC, sarcoma, cervical, and anal cancer
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Multiplex TCR-T cell therapy is designed to overcome the heterogeneity of solid tumors 23 Many solid tumors exhibit heterogeneity of target expression NSCLC Deep and durable responses may require TCR-T cell therapy for multiple targets Relapse Targeting long-term remission or cureSingle solid tumor expression of PRAME and MAGE-A4 MAGE-A4+ Singleplex TCR-T targeting PRAME Multiplex TCR-T for PRAME + MAGE-A4 PRAME+ Data on file
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TScan is building the ImmunoBank of TCRs to enable multiplex TCR-T cell therapy 24 Customized TCR-T cell therapy Cancer cells with different HLA types and targets T cells Cancer patient Profile tumor HLA Type ImmunoBank of therapeutic TCRs HLAs Targets • Determine HLA type and target expression in patient tumor • Manufacture and administer customized, multiplex TCR-T cell therapy
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PLEXI-T , a multi-arm basket Phase 1 trial in subjects with solid tumors (NCT05973487) 25 Long term follow-upEndpoint and safety monitoringEligibility screening Day -6 Day +1 Day +29 Day +753 Tumor testing Patient selection Manufacturing apheresis Infusion 1 Infusion 2 Subject screening Treatment Protocol Ex vivo TCR-T cell manufacturing and infusion Screening Protocol • Germline HLA testing • Tumor testing for target followed by testing for HLA loss Key eligibility criteria • Age >18 years • Relapsed/refractory solid tumor after treatment with or refusal of SoC therapies • Eligible for treatment on a Phase 1 study that requires lymphodepleting chemotherapy Key endpoints • Safety: Dose limiting toxicities, adverse events • Efficacy • Exploratory: T cell persistence LD: lymphodepletion with fludarabine x 4 days and cyclophosphamide x 3 days; SoC: standard of care therapy; HLA: human leukocyte antigen LD
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Tumor testing for target and testing for HLA loss Patient selection Infusions 1a +1b Infusions 2a +2b Subject screening with germline HLA testing Treatment Protocol Screening Protocol ClinicalTrials.gov Identifier: NCT05973487; LD: lymphodepletion with fludarabine x 4 days and cyclophosphamide x 3 days; SoC: standard of care therapy; HLA: human leukocyte antigen Phase 1 PLEXI-T : dosed first patients with ex vivo multiplex TCR-T and are now developing an in vivo engineering platform 26 Clinical eligibility screening TCR-T cell manufacturing apheresis Lymphodepletion Treatment; Endpoint & safety monitoring Long term follow-up Day -6 Day +1 Day +29 Day +753 28 days+ +
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Lentivirus Lentiviral in vivo technology addresses the key challenges of autologous TCR-T 27 In vivo engineering solves the key challenges of autologous TCR-T approaches • Lymphodepletion is not required • Off-the-shelf (no patient-specific manufacturing); lentivirus prepared in large batches with significantly reduced COGS • No vein-to-vein time • Promising early clinical data from in vivo CAR-T therapy In vivo lentiviral approach offers potential for long-term response • Modified lentiviruses specifically target T-cells in vivo and enable permanent integration of genetic cargo • Engineered T-cells express a cancer- specific TCR and form memory cells, driving long term anti-cancer activity T cell
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Autoimmunity represents an exciting area of unmet need with few validated targets 28 Multi-year collaboration using TargetScan to identify targets for T cells in patients with Crohn’s disease Identified targets for systemic sclerosis, ulcerative colitis, ankylosing spondylitis, and birdshot uveitis using proprietary platform • Current therapies typically provide general immune suppression, leading to complications (e.g., increased risk of infection) • Target-specific therapies provide a way to address the cause, rather than the symptoms, of autoimmunity • Many autoimmune disorders have a substantial T-cell component, but the targets of these pathogenic or protective T-cells are largely unknown • TScan’s target discovery platform provides a way to identify targets in autoimmune disease, unlocking the development of targeted therapeutics
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Executed on milestones in 2025, momentum continues into 2026 29 Aligned on final pivotal design for TSC-101 Two-year relapse data from initial TSC-101 patients Heme Program File two INDs for TSC-102 (A*03:01 and A*01:01) Opened expansion cohorts at DL3 Auto- immunity Identified novel autoantigens Presented preclinical data for lead programs Safety and response data from PLEXI-T trial in Q1 Solid Tumor Program First patients treated with multiplex TCR-T therapy Dose escalation completed for singleplex TCR-T tx Launch pivotal trial for TSC-101 in Q2 H2 2025 2026H1 2025 Proof-of-concept for therapeutic approach
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