Aprea Therapeutics, Inc. · NASDAQ:APRE

Aprea Therapeutics — Investor Presentation (November 2025)

20 slides from Aprea Therapeutics's investor presentation, Nov 12, 2025

Slide 1: Precision Oncology Through Synthetic Lethality
1 © 2025 Aprea Therapeutics, Inc. All Rights Reserved Precision Oncology Through Synthetic Lethality Transforming DDR Inhibition into Patient Benefit November 2025
Slide 2: Forward-Looking Statements
2 © 2025 Aprea Therapeutics, Inc. All Rights Reserved Forward-Looking Statements Certain information contained in this presentation includes “forward-looking statements”, within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 19
Slide 3: One Critical Pathway, Multiple Targets
3 © 2025 Aprea Therapeutics, Inc. All Rights Reserved One Critical Pathway, Multiple Targets Li et al., Nucleic Acids Research, 2024 Undisclosed Target Precision Medicine Synthetic Lethality Aprea
Slide 4: Robust DDR Development Pipeline
4 © 2025 Aprea Therapeutics, Inc. All Rights Reserved Robust DDR Development Pipeline Milestones 2024-2026 Accomplished And Anticipated Clinical Milestones 2024 2025 2026 H1 H2 H1 H2 H1 H2 ATR ATRN-119 WEE1 APR-1051 RP2D for QD dosing ACESOT-1051: Phase 1 – Monotherapy Dose Escalation Enrolled First
Slide 5: Strong Drug Development and Commercial Expertise
5 © 2025 Aprea Therapeutics, Inc. All Rights Reserved Strong Drug Development and Commercial Expertise Experienced Team in Synthetic Lethality and Targeted Therapy Management Board of Directors Richard Peters, M.D., Ph.D. Chairman of the Board Oren Gilad, Ph.D. President and CEO Jean-Pierre Bizzari,
Slide 7: ACESOT-1051: Phase 1 Study Design
7 © 2025 Aprea Therapeutics, Inc. All Rights Reserved Eligible patients ≥ 18 yo with advanced solid tumor harboring cancer-associated gene alterations CCNE1 or CCNE2 FBXW7 or PPP2R1A, KRAS-GLY12/GLY13 & TP53, and USC regardless biomarker status. HPV+ oropharyngeal squamous cell carcinoma, HPV+ cervi
Slide 8: ACESOT-1051: Summary of Duration of Treatment
8 © 2025 Aprea Therapeutics, Inc. All Rights Reserved 22 42 68 104 50 57 174 25 43 47 55 55 57 48 36 50 0 30 60 90 120 150 180 210 10 mg 20 mg 30 mg 50 mg 70 mg 100 mg ACESOT-1051: Summary of Duration of Treatment (n=16) Tolcher A. et al. Mol Cancer Ther (2025) 24 (10_Supplement): B011.. Not all dat
Slide 9: ACESOT-1051: Early Signals of Clinical Activity in Dose Escalation Study
9 © 2025 Aprea Therapeutics, Inc. All Rights Reserved ACESOT-1051: WEE1 Inhibitor, Single Agent Early Signals of Clinical Activity in Dose Escalation Study Dose Cohort Patients with SD Best Tumor Shrinkage/Patient 70 mg (n=3) 1 -5% 100 mg (n=4) 3 +15%, +1%, -13% Total 4 Initial clinical activity at
Slide 10: From Bench to Bedside #1: Preclinical Activity Observed in Early Patient Outcomes
10 © 2025 Aprea Therapeutics, Inc. All Rights Reserved From Bench to Bedside #1: Preclinical Activity Observed in Early Patient Outcomes Pre-clinical studies with APR-1051 Data on file APR-1051 shows single agent activity in cancer cells overexpressing Cyclin E n=7 mice per group, APR-1051, 30 mg/kg
Slide 11: From Bench to Bedside #2: Preclinical Activity Observed in Early Patient Outcomes
11 © 2025 Aprea Therapeutics, Inc. All Rights Reserved s si e s e e 100 80 0 40 20 0 0 10 20 30 Clinical Data 70 mg Cohort HPV+ HNSCC Mouse Model From Bench to Bedside #2: Preclinical Activity Observed in Early Patient Outcomes Patient: 52-year-old Male Diagnosis: HPV+ Oropharyngeal Squamous Cell Ca
Slide 12: APR-1051 Demonstrated Clinical Activity in Combination Across Multiple Cancer Models
12 © 2025 Aprea Therapeutics, Inc. All Rights Reserved HPV+ Cancer – Collaboration with MD Anderson Ovarian Cancer* UMSCC47 tumor cells OVCAR3 tumor xenograft Tumor Volume (mm3 ) Vehicle Aprea ATRi 30 mg/kg QD Aprea WEE1i 30 mg/kg QD Combination – half dose, 15mg/kg each Days Post Treatment Tumor Vo
Slide 14: ABOYA-119: Phase 1/2a Trial Design and Status
14 © 2025 Aprea Therapeutics, Inc. All Rights Reserved ABOYA-119: Phase 1/2a Trial Design and Status Patient Population: Male or female subjects 12 years of age or older with solid tumors harboring any DDR mutation per NGS (or Merkel Cell Carcinoma). Potential Combinations • Radiation therapy • Anti
Slide 15: From Bench to Bedside: Preclinical Activity Reflected in Early Patient Outcomes
15 © 2025 Aprea Therapeutics, Inc. All Rights Reserved From Bench to Bedside: Preclinical Activity Reflected in Early Patient Outcomes ATRN-119 shows single agent activity in cancer cells with ARID1A mutation 200mg Cohort -3.0 -2.5 -2.0 -1.5 -1.0 -0.5 0.0 0 20 40 60 80 100 Log10 [ATRN119] (μM) % Act
Slide 17: Intellectual Property, Financial Summary & Capitalization, Investment Highlights
17 © 2025 Aprea Therapeutics, Inc. All Rights Reserved 17 Intellectual Property Portfolio Financial Summary & Capitalization Investment Highlights
Slide 18: Robust Global Intellectual Property Protection
18 © 2025 Aprea Therapeutics, Inc. All Rights Reserved Robust Global Intellectual Property Protection Family 1: Ataxia Telengiectasia and Rad3-Related (ATR) Protein Kinase Inhibitors • Macrocyclic inhibitors of ATR & methods of using them to treat various cancers, filed on Oct. 13th, 2015 • Patents
Slide 19: Financial Summary & Capitalization
19 © 2025 Aprea Therapeutics, Inc. All Rights Reserved Securities Common Equivalents as of November 12, 2025 Preferred Stock (as converted) 15,596 Common Stock 1 6,310,673 Warrants: Pre-Funded Tranche A Tranche B Total 507,076 1,097,394 1,097,394 2,701,864 Options 811,121 Restricted Stock Units 31,0
Slide 20: Investment Highlights
20 © 2025 Aprea Therapeutics, Inc. All Rights Reserved Financed into Q4 2026 • Achieve near term inflection points and catalysts • Evaluate optimal strategic partnerships Near term catalysts • APR-1051: Q1 2026 Safety/efficacy data Q2 2026 Complete dose escalation • ATRN-119: Q4 2025 clinical update

Aprea Therapeutics — Investor Presentation (November 2025) on 6ix

Aprea Therapeutics — Investor Presentation (November 2025)

Slide 1: Precision Oncology Through Synthetic Lethality

Slide 2: Forward-Looking Statements

Slide 3: One Critical Pathway, Multiple Targets

Slide 4: Robust DDR Development Pipeline

Slide 5: Strong Drug Development and Commercial Expertise

Slide 6: WEE1 Inhibitor: APR-1051

Slide 7: ACESOT-1051: Phase 1 Study Design

Slide 8: ACESOT-1051: Summary of Duration of Treatment

Slide 9: ACESOT-1051: Early Signals of Clinical Activity in Dose Escalation Study

Slide 10: From Bench to Bedside #1: Preclinical Activity Observed in Early Patient Outcomes

Slide 11: From Bench to Bedside #2: Preclinical Activity Observed in Early Patient Outcomes

Slide 12: APR-1051 Demonstrated Clinical Activity in Combination Across Multiple Cancer Models

Slide 13: ATR Inhibitor: ATRN-119

Slide 14: ABOYA-119: Phase 1/2a Trial Design and Status

Slide 15: From Bench to Bedside: Preclinical Activity Reflected in Early Patient Outcomes

Slide 16: Aprea Therapeutics

Slide 17: Intellectual Property, Financial Summary & Capitalization, Investment Highlights

Slide 18: Robust Global Intellectual Property Protection

Slide 19: Financial Summary & Capitalization

Slide 20: Investment Highlights