Phase 1 Study to Evaluate Safety and Efficacy of APR-548 in Combination With Azacitidine for the Treatment of TP53-Mutant Myelodysplastic Syndromes
Phase: PHASE1
Conditions: MDS, Myelodysplastic Syndromes
Sponsor: Aprea Therapeutics

Aprea Therapeutics, Inc. 
Protocol Number A20-11202 
Phase 1 Study of APR-548 with Azacitidine in TP53-Mutant MDS 
 
1202_CSP_6.0 
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Phase 1 Study to Evaluate Safety and Efficacy of APR-548 in Combination with 
Azacitidine for the Treatment of TP53-Mutant Myelodysplastic Syndromes 
 
 
Protocol No.: 
A20-11202 
 
IND No.: 
150967 
 
 
 
 
Sponsor: 
Aprea Therapeutics, Inc. 
 
 
 
 
 
 
 
 
Responsible Medical Officer: 
 
 
 
 
Medical Monitor: 
 
 
 
 
 
Protocol Version: 
6.0 
 
Replaces: 
 
5.0 
Date: 
10 September 2021 
 
 
 
 
 
 
 
 
 
 
 
 
 
CONFIDENTIAL 
 
This document contains strictly confidential information and cannot be disclosed or used, 
unless authorized in writing by Aprea Therapeutics, Inc. 
 

Aprea Therapeutics, Inc. 
Protocol Number A20-11202 
Phase 1 Study of APR-548 with Azacitidine in TP53-Mutant MDS 
 
1202_CSP_6.0 
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Name: 
 
 
Telephone: 
 
 
 
 
 
 
Address: 
 
 
 
 
 
 
 
 
 
Signature: 
 
 
Date: 
 
 
 
 
 
INVESTIGATOR’S STATEMENT 
1. 
I have carefully read this protocol entitled “Phase 1 Study to Evaluate Safety and Efficacy 
of APR-548 in Combination with Azacitidine for the Treatment of TP53-Mutant 
Myelodysplastic Syndromes” and agree that it contains all the necessary information 
required to conduct the study. I agree to conduct this study as outlined in the protocol. 
2. 
I understand that this study will not be initiated without approval of the appropriate 
Institutional Review Board (IRB)/Independent Ethics Committee (IEC), and that all 
administrative requirements of the governing body of the Institution will be complied with 
fully. 
3. 
Informed written consent will be obtained from all participants in accordance with 
institutional guidelines, United States (US) Food and Drug Administration (FDA) 
requirements as specified in Title 21 Code of Federal Regulations (CFR), Part 50, the 
European Union Directive 2001/20/European Commission (EC) and its associated Detailed 
Guidances, European Union Good Clinical Practice (GCP) Directive 2005/28/EC, the 
International Council for Harmonization (ICH) Guideline for GCP, Section 4.8, and the terms 
of the Declaration of Helsinki (2013). 
4. 
I will enroll participants who meet the protocol criteria for entry. 
5. 
I understand that my signature on each completed electronic Case Report Form (eCRF) 
indicates that I have carefully reviewed the complete set of eCRFs and accept full 
responsibility for the contents thereof. 
6. 
I understand that the information presented in this study protocol is confidential, and I 
hereby assure that no information based on the conduct of the study will be released 
without prior consent from the Sponsor unless this requirement is superseded by the FDA, 
a Competent Authority of the European Union or another Regulatory Authority. 
 
Protocol Version 6.0: 10 September 2021 

Aprea Therapeutics, Inc. 
Protocol Number A20-11202 
Phase 1 Study of APR-548 with Azacitidine in TP53-Mutant MDS 
 
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Protocol Number A20-11202 
Phase 1 Study of APR-548 with Azacitidine in TP53-Mutant MDS 
 
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TABLE OF CONTENTS 
        Page No. 
INVESTIGATOR’S STATEMENT .................................................................................................. 2 
TABLE OF CONTENTS ............................................................................................................... 4 
CLINICAL STUDY SYNOPSIS ..................................................................................................... 9 
LIST OF ABBREVIATIONS ........................................................................................................ 22 
1.0 
GENERAL INFORMATION ......................................................................................... 24 
1.1 Protocol Number and Title of the Study ...................................................................... 24 
1.2 Sponsor ........................................................................................................................... 24 
1.3 Medical Monitor ............................................................................................................. 24 
1.4 Signature Authorization ................................................................................................ 24 
2.0 
BACKGROUND INFORMATION ................................................................................ 24 
2.1 Disease Background ...................................................................................................... 24 
2.2 TP53 Mutations in MDS .................................................................................................. 25 
2.3 APR-548 ........................................................................................................................... 25 
2.3.1 Pharmacology and Mode of Action ................................................................. 26 
2.3.2 Pharmacokinetics .............................................................................................. 27 
2.3.3 Safety Pharmacology and Toxicology ............................................................. 28 
2.4 Azacitidine ....................................................................................................................... 29 
2.5 Rationale for the Starting Dose and Maximum Exposure of APR-548 ..................... 30 
2.6 Rationale for Combination of APR-548 with Azacitidine ............................................ 31 
2.7 Rationale for Dose of APR-548 in Combination with Azacitidine ............................. 31 
2.8 Potential Risks and Benefits .......................................................................................... 31 
2.8.1 Potential Risks .................................................................................................... 31 
2.8.2 Potential Benefits .............................................................................................. 34 
2.9 Characteristics of a Well-Conducted Trial ................................................................... 34 
2.10 Subject Population ......................................................................................................... 35 
3.0 
TRIAL OBJECTIVES AND PURPOSE ........................................................................... 35 
3.1 Primary Objective ........................................................................................................... 35 
3.2 Secondary Objectives .................................................................................................... 35 
4.0 
TRIAL DESIGN ............................................................................................................ 36 
4.1 Overview of Trial Design ................................................................................................ 36 
4.1.1 Treatment Duration .......................................................................................... 38 
4.2 End of Study .................................................................................................................... 39 
4.3 Drug Products ................................................................................................................. 39 
4.3.1 APR-548 ............................................................................................................... 39 
4.3.2 Azacitidine .......................................................................................................... 39 
4.4 Duration of Therapy....................................................................................................... 40 
4.5 Trial Discontinuation ...................................................................................................... 40 

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Phase 1 Study of APR-548 with Azacitidine in TP53-Mutant MDS 
 
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4.6 Drug Accountability/Disposition of APR-548 Supplies ............................................... 40 
4.7 Inclusion Criteria ............................................................................................................ 41 
4.8 Exclusion Criteria ............................................................................................................ 42 
4.9 Inclusion of Women, Minorities and Children ............................................................ 43 
4.10 Withdrawal Criteria ........................................................................................................ 43 
4.10.1 Study Treatment Discontinuation ................................................................... 43 
4.10.2 Subject Withdrawal from Study Treatment .................................................... 44 
4.10.3 Study Completion .............................................................................................. 44 
4.10.4 Subject Withdrawal from Study ....................................................................... 44 
4.10.5 Withdrawn Subjects .......................................................................................... 44 
4.11 Noncompliance .............................................................................................................. 44 
5.0 
TREATMENT OF SUBJECTS ........................................................................................ 44 
5.1 Drug Preparation and Administration ......................................................................... 44 
5.1.1 APR-548 ............................................................................................................... 45 
5.1.2 Azacitidine .......................................................................................................... 45 
5.1.3 Dose-Limiting Toxicity ....................................................................................... 45 
5.1.4 Dose Escalation Strategy .................................................................................. 46 
5.2 Dose Interruptions/Withholding .................................................................................. 47 
5.3 Supportive Management ............................................................................................... 55 
5.3.1 Growth Factors .................................................................................................. 55 
5.3.2 Blood Products .................................................................................................. 55 
5.3.3 Management of Infection and/or Infestation Event(s) .................................. 56 
5.3.4 Management of Neutropenia with or without Fever .................................... 56 
5.3.5 Management of Nausea, Vomiting and Diarrhea .......................................... 57 
5.3.6 Management of CNS-Related Adverse Events ............................................... 57 
5.4 Concomitant Treatment ................................................................................................ 57 
5.5 Monitoring Subject Compliance ................................................................................... 58 
6.0 
STUDY EVALUATIONS ............................................................................................... 58 
6.1 Schedule of Study Assessments ................................................................................... 58 
6.2 Pre-Study Assessments ................................................................................................. 63 
6.3 Screening ......................................................................................................................... 63 
6.4 Safety Run-In Period (APR-548 Monotherapy) ............................................................ 63 
6.4.1 Day 1 ................................................................................................................... 63 
6.4.2 Days 2 – 4 ............................................................................................................ 64 
6.4.3 Day 5 ................................................................................................................... 64 
6.4.4 Day 8 ................................................................................................................... 64 
6.4.5 Day 15 ................................................................................................................. 65 
6.4.6 Day 21 ................................................................................................................. 65 
6.4.7 Day 28 ................................................................................................................. 65 
6.5 Cycle 1 (APR-548 + Azacitidine Safety Run-In Period) ................................................ 66 
6.5.1 Day 1 ................................................................................................................... 66 
6.5.2 Days 2 – 4 ............................................................................................................ 66 

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Phase 1 Study of APR-548 with Azacitidine in TP53-Mutant MDS 
 
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6.5.3 Days 5 – 7 ............................................................................................................ 66 
6.5.4 Day 8 ................................................................................................................... 67 
6.5.5 Day 15 ................................................................................................................. 67 
6.5.6 Day 22 ................................................................................................................. 67 
6.6 Cycle 2.............................................................................................................................. 68 
6.6.1 Day 1 ................................................................................................................... 68 
6.6.2 Days 2 – 7 ............................................................................................................ 68 
6.6.3 Day 8 ................................................................................................................... 69 
6.6.4 Day 15 ................................................................................................................. 69 
6.7 Cycle 3 and Onwards ..................................................................................................... 69 
6.7.1 Day 1 ................................................................................................................... 69 
6.7.2 Days 2 – 7 ............................................................................................................ 70 
6.7.3 Day 15 ................................................................................................................. 70 
6.8 End of Treatment Visit ................................................................................................... 70 
6.9 Long-Term Follow-Up .................................................................................................... 71 
7.0 
STUDY ASSESSMENTS ............................................................................................... 71 
7.1 Safety Assessments ....................................................................................................... 71 
7.1.1 Safety Analysis ................................................................................................... 71 
7.1.2 Reporting of Adverse Events ............................................................................ 72 
7.2 Efficacy Assessments ..................................................................................................... 76 
7.2.1 Complete Remission Rate ................................................................................. 76 
7.2.2 Duration of Response ....................................................................................... 76 
7.2.3 Overall Response ............................................................................................... 76 
7.2.4 Overall Survival .................................................................................................. 76 
7.2.5 Relapse-Free Survival ........................................................................................ 76 
7.2.6 Rate of AML Transformation, Transition to HSCT, and Transfusion 
Independence ................................................................................................................ 76 
7.3 Pharmacokinetics ........................................................................................................... 77 
7.4 Pharmacodynamics ....................................................................................................... 78 
7.5 Electrocardiographic Assessment ................................................................................ 79 
7.6 Ophthalmological Evaluation ........................................................................................ 80 
8.0 
STATISTICS ................................................................................................................. 80 
8.1 Sample Size ..................................................................................................................... 81 
8.2 Analysis Populations ...................................................................................................... 81 
8.3 Endpoints ........................................................................................................................ 81 
8.3.1 Primary ............................................................................................................... 81 
8.3.2 Secondary ........................................................................................................... 81 
8.3.3 Exploratory ......................................................................................................... 82 
8.4 Safety Stopping Criteria ................................................................................................. 82 
8.5 Safety ............................................................................................................................... 82 
8.6 Efficacy ............................................................................................................................. 83 
8.7 Pharmacokinetic Analysis.............................................................................................. 83 

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8.8 Exploratory analyses ...................................................................................................... 84 
9.0 
QUALITY CONTROL AND QUALITY ASSURANCE PROCEDURES ............................ 84 
9.1 Monitoring of the Study and Regulatory Compliance ................................................ 84 
9.2 Curricula Vitae and Financial Disclosure of Investigators ......................................... 85 
9.3 Protocol Modifications ................................................................................................... 85 
9.4 Publication Policy ........................................................................................................... 85 
10.0 
ETHICAL CONSIDERATIONS ..................................................................................... 85 
10.1 Informed Consent .......................................................................................................... 85 
10.2 Institutional Review Board/Independent Ethics Committee ..................................... 86 
10.3 Subject Privacy ................................................................................................................ 86 
11.0 
DATA HANDLING AND RECORDKEEPING ............................................................... 86 
11.1 Data to be Entered Directly in the Case Report Form................................................ 86 
11.2 Recording of Data .......................................................................................................... 86 
11.3 Study Records ................................................................................................................. 87 
12.0 
REFERENCES .............................................................................................................. 88 
APPENDIX I - Cockcroft-Gault Equation .............................................................................. 92 
APPENDIX II - ECOG Performance Status ............................................................................ 93 
APPENDIX III - Acceptable Contraceptive Methods ........................................................... 94 
APPENDIX IV - New York Heart Association (NYHA) Classification ................................. 95 
APPENDIX V - Response Criteria for Subjects with MDS and CMML According to IWG 
2006 Criteria39 ......................................................................................................................... 96 
APPENDIX VI - 2016 WHO Classification for CMML and MDS40 WHO CMML ................... 98 
APPENDIX VII – TP53 Sequence Variant Interpretation Algorithm ................................ 100 
 
 
List of In-text Tables  
Table 1. Dose escalation parameters ........................................................................................... 37 
Table 2. Dose management guidelines for new onset hematologic toxicities ........................ 48 
Table 3. Dose management guidelines for non-hematologic toxicities ................................... 48 
Table 4. APR-548 and azacitidine dose management guidelines for infection and/or 
infestation adverse events ............................................................................................................ 49 
Table 5. APR-548 dose management guidelines for nausea, vomiting, and/or diarrhea 
adverse events ................................................................................................................................ 49 
Table 6. Dose management guidelines for APR-548 and azacitidine for worsening 
neutropenia from baseline with or without fever ...................................................................... 50 
Table 7. Management of ocular-associated adverse events ..................................................... 51 
Table 8. Management of CNS adverse events (e.g., dizziness, tremor, confusion, and ataxia)
 .......................................................................................................................................................... 52 

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Table 9. Management of serum creatinine elevations and acute kidney injury ..................... 53 
Table 10. Management of liver enzymes elevation .................................................................... 54 
Table 11. Recommendations for prevention and treatment of cancer-related infections .... 56 
Table 12. Schedule of assessments .............................................................................................. 59 
Table 13. PK blood sampling timepoints for APR-548 and azacitidine in the safety run-in 
period and subsequent cycles ...................................................................................................... 77 
Table 14. PK blood sampling timepoints for MQ-H2O, MQ-Cys and MQ-GSH for subjects at 
selected centers .............................................................................................................................. 78 
Table 15. ECG assessment requirements .................................................................................... 79 
Table 16. Ophthalmological evaluation ....................................................................................... 80 
Table 17. Basic parameters for TP53 sequencing and interpretation. ................................... 100 
Table 18. Listing of synonymous variants with pathogenic splice impact ............................. 103 
Table 19. Listing of benign or likely benign TP53 variants to be used for exclusion ............ 103 
 
 
List of In-text Figures 
Figure 1. Dose escalation schema for the safety run-in and combination portion ................ 11 
Figure 2. APR-548 structural formula of the drug substance .................................................... 26 
Figure 3: Structural relationship between APR-548, APR-246 and MQ .................................... 27 
Figure 4. Algorithm for TP53 variant interpretation. ................................................................ 101 
 
 

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Phase 1 Study of APR-548 with Azacitidine in TP53-Mutant MDS 
 
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CLINICAL STUDY SYNOPSIS 
Title 
Phase 1 Study to Evaluate Safety and Efficacy of APR-548 in Combination with 
Azacitidine for the Treatment of TP53-Mutant Myelodysplastic Syndromes 
Sponsor 
Aprea Therapeutics, Inc. 
Monitor/ 
Contract 
Research 
Organization 
(CRO) 
 
Number of 
Study Centers 
Up to 10 
Clinical Phase 
1 
Sample Size 
Up to 46 subjects 
Investigational 
Agent 
APR-548 
Study Design 
This is an open-label first-in-human (FIH) phase 1 clinical trial that utilizes a standard 
3 + 3 design. The study will assess safety, pharmacokinetics (PK), and clinical activity 
of orally (p.o.) administered APR-548 alone and in combination with azacitidine for 
the treatment of TP53-mutant myelodysplastic syndromes (MDS). 
 
Safety Run-In Periods (28-day cycles) 
Safety Run-In Monotherapy: 3+3 dose escalation of APR-548 as monotherapy on 
Days 1-4. 
Safety Run-In Combination Therapy: 3+3 dose escalation of APR-548 in combination 
with azacitidine. APR-548 on Days 1-4 in combination with azacitidine on Days 1-7. 
 
APR-548 will initially be given p.o. once daily (QD) during Days 1 – 4 of a 28-day safety 
run-in period. The first 3 subjects enrolled on each dose level will be evaluated for a 
28-day dose-limiting toxicity (DLT) safety follow-up period prior to enrolling 
additional subjects on that dose level or prior to dose escalation. If no DLT is 
observed, subjects will proceed to the safety run-in combination therapy portion 
with APR-548 in combination with azacitidine administered subcutaneously (s.c.) or 
intravenously (i.v.) at the standard dose of 75 mg/m2 on Days 1-7 of the 28-day cycle. 
The first 3 subjects on each dose level of the combination with APR-548 and 
azacitidine will be evaluated for a 28-day DLT safety follow-up period prior to dose 
escalation with the combination treatment.  
 
During the safety run-in of the monotherapy and during the safety run-in of the 
combination treatment, each subject within the dose level will be evaluated for 
safety and tolerability of APR-548. APR-548 dose escalation will be guided by an 
assessment of safety, PK and pharmacodynamic (PD) data, and may proceed until 
DLTs are observed, or the pre-defined maximum exposure of APR-548 in plasma 

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Protocol Number A20-11202 
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(average maximum concentration [Cmax] and area under the curve [AUC] 8 μM and 
16 μM·h, respectively) is reached, or the minimum biologically effective dose (mBED) 
is achieved (the dose at which no further incremental effect on markers of apoptosis 
and/or proliferation is observed, in the monotherapy safety run-in only). The Data 
Review Team (DRT), consisting of the Medical Monitor, Site Principal Investigators, 
retina specialist and other clinical research personnel that the Sponsor deems 
appropriate, will review the available PK, PD and safety data for each 3-6 subject 
cohort in both the safety run-in for the monotherapy and the combination portions, 
and increases in dose will be guided by the observed safety, PK and PD data, until 
the recommended phase 2 dose (RP2D) is determined. The RP2D of APR-548 will be 
defined as the lowest of: 
1. The mBED in the monotherapy safety run-in, 
2. The dose that achieves the pre-defined level of maximum exposure in the 
monotherapy or combination therapy safety run-ins, or 
3. The dose at which there are <2 DLTs in 3-6 subjects in a cohort, in the 
monotherapy or combination therapy safety run-ins. 
 
Up to 10 subjects may be enrolled at the RP2D per decision of the DRT to gain 
additional confidence in the RP2D. 
 
Subjects in Cohort 1 will receive a starting APR-548 dose of 50 mg/day (Dose level 1). 
If there is a DLT in ≤1/3 subjects in Cohort 1, Cohort 1 will be expanded to enroll 3 
more subjects. If ≥2 subjects out of the total 3–6 subjects have a DLT, dose escalation 
will not occur. If ≤1 DLT occurs in the 6 subjects treated at that dose level, the 
subsequent subject group (Cohort 2) will be enrolled upon DRT review of data as 
described above, at the APR-548 dose of 150 mg/day (Dose level 2). If ≥2 of 6 subjects 
at a dose level have a DLT, or if the pre-defined maximum exposure of APR-548 in 
plasma is reached or the minimum biological effective dose is achieved (in 
monotherapy safety run-in only), then dose escalation ceases. This study will 
evaluate up to 6 dose levels.  Any subsequent dose escalation will not exceed 100% 
and will follow the same cohort escalation plan as outlined above and in Figure 1. 
 

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Figure 1. Dose escalation schema for the safety run-in and 
combination portion 
Cohort 1 – Dose Level 1 (APR-548 50 mg/day); Cohort 2 – Dose Level 2 (APR-548 150 mg/day);  
Cohort 3 – Dose Level 3 (APR-548 300 mg/day).  
Additional cohorts may be added utilizing the same dose escalation scheme 
 
Dose-Limiting Toxicity 
All treatment-emergent adverse events (TEAEs) are relevant to the determination of 
DLTs unless they are clearly and solely due to the disease under study. During the 
28-day safety run-in period for APR-548 monotherapy and during the 28-day safety 
run-in period for APR-548 in combination with azacitidine, a DLT is defined as any of 
the following TEAEs defined by the National Cancer Institute Common Terminology 
Criteria for Adverse Events (NCI-CTCAE), as follows:   
 
• 
Non-hematological NCI-CTCAE ≥Grade 3 adverse event (AE), including ocular 
AEs that are different from retinopathy or optic nerve disorder classifications.  
• 
Prolonged myelosuppression with the persistence of ≥Grade 4 neutropenia or 

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thrombocytopenia in the absence of disease lasting 14 days from the initial 
administration of APR-548 (only during the safety run-in period for APR-548 
monotherapy). 
• 
Grade 3 nausea/vomiting/diarrhea/fatigue/central nervous system (CNS) AE. 
Grade 3 nausea/vomiting/diarrhea may be excluded if parenteral nutrition, 
tube feeding, or prolonged hospitalization is not required. 
• 
New or worsening retinopathy or optic nerve disorder AE of any grade. 
• 
Grade 3 metabolic/electrolyte abnormalities that do not resolve to ≤Grade 1 or 
baseline within 72 hours. 
• 
Grade ≥4 neutropenia lasting past day 28 in the absence of disease. 
• 
Any AE, regardless of the NCI-CTCAE Grade, resulting in discontinuation, dose 
reduction or treatment with less than 75% of planned doses of APR-548, unless 
clearly and solely related to the disease under study. 
 
Investigator should contact the Medical Monitor to discuss any findings suggestive 
of ocular-associated AEs. Any ≥Grade 2 ocular-associated AEs are considered AEs of 
special interest and should be reported as serious adverse events (SAEs). Subjects 
with signs and/or symptoms of vision changes should be seen immediately by 
ophthalmologist/retinal specialist. APR-548 may be permanently discontinued, 
following a discussion with the Medical Monitor, if: 
• 
Any retinopathy or optic nerve disorder develops, regardless of perceived 
attribution to study drug, and  
• 
A clinical retina specialist or ophthalmologist determines a retinal or optic 
nerve finding is substantially changed from the subject's baseline test. 
 
Additionally, TEAEs that meet the above criteria, but occur after the DLT evaluation 
period will not be defined as DLTs, but will be reported as AEs/SAEs and will be 
reviewed across all cohorts during the study to help determine the AE profile for the 
respective treatment regimens under study. A subject that discontinues APR-548 
therapy during the DLT assessment period without DLT is considered evaluable for 
the purpose of safety only if at least 75% of the scheduled dose of APR-548 was 
administered in the monotherapy safety run-in period. 
 
The DRT will also review any other emergent toxicities that are not explicitly defined 
by the DLT criteria to determine if any warrant a DLT designation. 
 
Following discussions with the DRT, the schedule of APR-548 may be modified, 
including multiple daily and weekly doses, based on available PK, PD, and safety data. 
 
Subjects may continue treatment as long as safety remains acceptable, progression 
has not occurred, and the subject has not withdrawn consent. Response and 
progressive disease will be assessed based on the Guidelines for Implementation of 
International Working Group (IWG) response criteria (Appendix V) after every two 
treatment cycles for the first year of study treatment, then every three cycles 
thereafter. Subjects may remain on study treatment after relapse or progression if 
they are continuing to derive clinical benefit in the opinion of the investigator. 

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Investigators may choose to transition subjects towards a stem cell transplantation 
(SCT) as appropriate after a response by the study treatment has been achieved. 
Subjects who undergo SCT will be removed from study treatment and will be 
followed per the study calendar. 
 
 Study 
Objectives 
Primary objective:   
To investigate the PK, safety and tolerability of APR-548 as monotherapy and in 
combination with azacitidine and determine the RP2D of APR-548 in subjects with 
TP53-mutant MDS. 
 
Secondary objectives: 
1. To assess preliminary clinical activity of APR-548 administered in combination 
with azacitidine:  
a. Rate of complete remission (CR) 
b. Duration of CR (DOCR) 
c. Overall response rate (ORR) 
d. Duration of ORR 
e. Rate of and time to development of acute myeloid leukemia (AML), as 
defined World Health Organization (WHO) criteria 
f. 
Overall survival (OS) 
g. Relapse-free survival (RFS) 
h. Rate of transition to hematopoietic stem cell transplant (HSCT) 
i. 
Rate of red blood cell (RBC) and/or platelet transfusion independence (TI) 
for 8 weeks 
2. To characterize PK of APR-548 after single and multiple dosing when given p.o. 
3. To evaluate the PK drug-drug interaction between APR-548 and azacitidine. 
 
Exploratory objectives: 
1. To assess PD markers of APR-548 in blood and bone marrow samples. 
2. To assess molecular markers of response to APR-548 in baseline and serial blood 
samples and bone marrow samples. 
 
Study 
Endpoints 
Primary endpoints: 
1. Occurrence of DLTs, classified and graded according to the NCI-CTCAE 
version 5.0 
2. Frequency of TEAEs and SAEs related to APR-548 alone and in combination with 
azacitidine 
3. RP2D of APR-548 
  
Secondary endpoints: 
1. Rate of CR 
2. DOCR, defined as the time from documentation of CR to disease relapse 
3. Duration of response (DOR), defined as the time from documentation of tumor 
response to disease relapse/progression or death as a result of any cause 
4. ORR is the proportion of subjects achieving hematological improvement (HI), 
partial remission (PR), CR, marrow CR by modified IWG 2006 criteria 
5. Rate of and time to AML transformation, according to WHO criteria 

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6. OS 
7. RFS 
8. Proportion of subjects who transition to HSCT 
9. Subjects who achieve RBC and/or platelet TI during the 8-week period after 
enrollment 
10. PK parameters: Cmax, time to Cmax (Tmax), AUC, oral volume of distribution (Vd/F), 
oral clearance (CL/F) and elimination half-life (T1/2) of APR-548 in the absence and 
presence of azacitidine 
11. PK parameters: Cmax, Tmax, AUC, T1/2 of APR-548 and the metabolites M8 (reduced 
MQ-glutathione adduct), M10 (reduced MQ-cysteine adducts), MQ water adducts 
(MQ-H2O) and MQ glutathione adducts (MG-GSH) 
 
Exploratory endpoints: 
1. PD markers of APR-548 may be explored using flow cytometry and molecular 
techniques including, but not limited to, markers of apoptosis and proliferation 
2. Exploratory analyses of molecular markers of response may include: TP53 
variant allele frequency (VAF) by next-generation sequencing (NGS), mutations 
and VAF of other genes by NGS, and gene and protein expression 
 
Eligibility 
criteria 
Inclusion criteria: 
 
1. Provision of signed and dated, written informed consent prior to any study 
specific procedures. 
2. Documented diagnosis of TP53-mutant MDS, according to WHO criteria that is 
previously untreated and meets IPSS-R classification of intermediate, high, or 
very high risk disease, or TP53-mutant MDS that is relapsed and/or refractory to 
prior treatments. Eligible TP53 mutations are defined in Appendix VII. 
3. Adequate organ function as defined by the following laboratory values: 
a. Creatinine clearance ≥60 mL/min (by Cockcroft-Gault method, Appendix I), 
b. Total serum bilirubin ≤1.5 × upper limit of normal (ULN) unless due to 
Gilbert’s syndrome or MDS organ involvement,  
c. Alanine aminotransferase and aspartate aminotransferase ≤2.5 × ULN, 
unless due to MDS organ involvement. 
4. Age ≥18 years at the time of signing the informed consent form. 
5. Eastern Cooperative Oncology Group (ECOG) performance status of 0, 1 or 2 
(Appendix II). 
6. Projected life expectancy of ≥12 weeks. 
7. Clear ocular media and adequate pupil dilation to permit fundus examination 
and retinal imaging. 
8. Female subjects must be surgically sterile, postmenopausal (for at least 1 year), 
or have negative results for a pregnancy test at screening, on a serum or urine 
sample obtained within 7 days prior to initiation of study treatment. 
9. Heterosexual female subjects of childbearing potential must agree to use 
adequate contraception or practice sexual abstinence as the preferred and 
usual lifestyle of the subject during the study and for up to 90 days after study 
treatment discontinuation. Adequate contraception is defined by the 
concomitant use of 2 effective methods of contraception, which can be 

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comprised of two barrier methods, or a barrier method plus a hormonal method 
or an intrauterine device that meets <1% failure rate for protection from 
pregnancy in the product label (Appendix III). Females of non-childbearing 
potential are those who are postmenopausal greater than 1 year or who have 
had a bilateral tubal ligation or hysterectomy or bilateral oophorectomy. Female 
subjects must refrain from egg cell donation while on study treatment and for 
at least 90 days after the last dose of APR-548 or azacitidine, whichever is longer. 
10. Male subjects with female partners of childbearing potential must have had a 
prior vasectomy or agree to use an adequate method of contraception (i.e., 
double barrier method: condom plus spermicidal agent) starting with the first 
dose of study therapy through 90 days after the last dose of APR-548 or 
azacitidine, whichever is longer. Male subjects should agree to refrain from 
sperm donation during the study and for at least 90 days after the last dose of 
APR-548 or azacitidine, whichever is longer. Should a female partner of a male 
subject become pregnant or suspect she is pregnant while participating in the 
study, he should inform his treating physician and the female partner should 
contact her physician immediately. 
 
Exclusion criteria: 
1. Any of the following cardiac abnormalities: 
a. Myocardial infarction within six months prior to enrollment; 
b. New York Heart Association Class III or IV heart failure (Appendix IV) or 
known left ventricular ejection fraction <40%; 
c. A history of familial long QT syndrome; 
d. Symptomatic atrial or ventricular arrhythmias not controlled by 
medications; 
e. Corrected QT interval Fridericia's formula (QTcF) ≥470 msec, unless due to 
underlying bundle branch block and/or pacemaker and with the approval 
of the Medical Monitor.  
2. Concomitant malignancies or previous malignancies with less than a 1-year 
disease-free interval at the time of signing informed consent. Subjects with 
adequately treated basal or squamous cell carcinoma of the skin, or adequately 
treated carcinoma in situ (e.g., cervix) may enroll irrespective of the time of 
diagnosis. Subjects with controlled, advanced prostate cancer are permitted. 
3. Known hypersensitivity to mannitol. 
4. Known hypersensitivity to fluorescein sodium. 
5. Use of cytotoxic chemotherapeutic agents, or experimental agents for the 
treatment of TP53-mutant MDS within 14 days or 5 half-lives of the product 
(whichever is shorter) of the first day of study drug treatment.  
6. Prior exposure to eprenetapopt (APR-246). 
7. Ongoing or prior history of ocular or hepatic graft-versus-host disease following 
allogeneic SCT. Subjects receiving systemic immunosuppressive therapy for 
treatment of (not prophylaxis) of graft-versus-host disease must be off systemic 
immunosuppressive therapy for a minimum of 6 weeks. 

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8. A female subject who is pregnant or breast-feeding. 
9. Known history of human immunodeficiency virus, active hepatitis B or active 
hepatitis C infection. 
10. Malabsorption syndrome or other condition likely to affect gastrointestinal 
absorption of APR-548.  
11. Known history or current evidence of ocular disease in either eye that, in the 
opinion of the investigator, may confound retinal assessments (e.g., glaucoma, 
advanced age-related macular degeneration, diabetic retinopathy, uveitis, or the 
presence of any condition that precludes adequate visualization of the fundus 
such as dense cataracts or corneal scarring). 
12. Family history of Leber hereditary optic neuropathy, autosomal dominant optic 
atrophy, late-onset retinal degeneration, familial dysautonomia or other 
hereditary mitochondrial disease, unless the causative mutation(s) in the family 
have been determined and the participant has tested negative for the 
mutation(s). 
13. Known prior or current retinal or optic nerve disease (e.g., retinitis pigmentosa, 
diabetic retinopathy, optic neuritis) that could impact interpretation of new 
onset retinal or optic nerve disease. 
14. Corrected visual acuity worse than 20/40. 
15. Other severe acute or chronic medical or psychiatric condition or laboratory 
abnormality that, in the opinion of the investigator, may increase the risk 
associated with study participation or study treatment administration or may 
interfere with the interpretation of study results and/or would make the subject 
inappropriate for enrollment into this study. 
16. Active uncontrolled infection.   
 
Treatment 
Plan 
Treatment will be administered on an outpatient basis but may be administered in 
the inpatient setting for subjects who are hospitalized and meet criteria for 
treatment. No investigational or commercial agents or therapies other than those 
described below may be administered with the intent to treat the subject's disease 
under study.  
 
In the 28-day safety run-in period, APR-548 will be given p.o. QD on Days 1 through 
4. Following discussions with the DRT, the schedule of APR-548 may be modified, 
including multiple daily and weekly doses. Following the 28-day safety run-in period, 
subjects proceed to the combination portion. 
 
In the combination portion, APR-548 will be given p.o. QD on Days 1 through 4 of 
each 28-day cycle. Azacitidine will be given at the standard dose of 75 mg/m2 over 7 
consecutive days (Days 1-7) as a s.c. injection or i.v. infusion. Following discussions 
with the DRT, the schedule of APR-548 may be modified, including multiple daily and 
weekly doses. 
 
Subjects in the 28-day safety run-in periods will be followed for at least 28 days 
before the safety of each cohort can be fully assessed and decisions made for dose 

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escalation in the next cohort. The mBED of APR-548 will be defined as the dose at 
which no further incremental effect on markers of apoptosis and/or proliferation is 
observed. Dose escalation of the monotherapy safety run-in may proceed until the 
earliest occurrence of 1) the mBED is reached, 2) ≥2 DLTs in 3-6 subjects in a cohort, 
or 3) average APR-548 exposure of exceeds 1/10 of the no-observed-adverse-effect 
level (NOAEL) or 1/5 the NOAEL for an individual subject (NOAEL relates to the dose 
level at which no AEs including eye toxicity were observed in the dog). For subjects 
that proceed from the monotherapy safety run-in to the combination safety run-in, 
if the dose escalation of the 28-day safety run-in proceeds more rapidly than the 
combination portion such that the dose of APR-548 undergoing evaluation in the 28-
day safety run-in exceeds that being assessed in the combination portion, the 
subject will receive the dose of APR-548 currently being assessed for safety in the 
combination portion. If a subject in the 28-day safety monotherapy run-in period has 
a dose reduction of APR-548 due to an AE, the subject will proceed with the reduced 
dose of APR-548 in the combination safety run-in of APR-548 with standard dose 
azacitidine. Dose escalation of the combination safety-run in may proceed until the 
earliest occurrence of 1) ≥2 DLTs in 3-6 subjects in a combination cohort, or 2) 
average APR-548 exposure in a combination cohort exceeds 1/10 of the NOAEL or 
1/5 the NOAEL for an individual subject. In addition, the dose of APR-548 in the 
combination portion will not exceed the mBED established in the monotherapy 
safety run-in. 
 
Cohort 
Dose Level a 
APR-548 (mg) b 
Expected Human PK 
Safety Factor to APR-
548 exposure at 
NOAEL in Dogs 
Cmax (μM) 
AUC 
(h·μM) 
Cmax (74.3 
μM) 
AUC (160 
h·μM) 
1 
1 (Starting 
dose) 
50 mg/day 
1.2 
2.7 
62 
59 
2 
2 
150 mg/day 
3.7 
8 
20.1 
20 
3 
3 
300 mg/day 
7.4 
16 
10 
10 
4 
4 
450 mg/day c 
11.1 
24 
6.7 
6.7 
Max dose 
Average limit 
8 
16 
9.2 
10 
Max dose 
Individual limit 
15 
32 
5 
5 
a Additional cohorts may be added guided by the DRT, with maximum exposure not exceeding 
pre-specified threshold 
b Dose levels are preliminary. Exact dose levels will be determined on safety and exposure data 
c Expected Human PK will be updated based on ongoing PK analysis and dose level of 450 mg/day 
will only be administered if expected human PK is below pre-specified thresholds after this update. 
 
Subjects in the combination portion may receive a higher dose of APR-548 than 
originally assigned after completion of at least two cycles of combination therapy at 
the assigned dose level if safety data for a higher dose level of APR-548 in 
combination with azacitidine have been reviewed by the DRT and concluded as safe. 
 
Subjects in the 28-day safety run-in periods (monotherapy or combination portions) 
who miss ≥25% of APR-548 doses for a nonmedical reason (e.g., subject’s 
preference) or noncompliance will be replaced. 
 

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The RP2D of APR-548 will be defined as the lowest of: 1) the mBED in the 
monotherapy safety run-in, 2) the dose that achieves the pre-defined level of 
maximum exposure in the monotherapy or combination therapy safety run-ins, or 
3) the dose at which there are <2 DLTs in 3-6 subjects in a cohort, in the monotherapy 
or combination therapy safety run-ins. 
Duration of 
Follow-Up  
 
Subjects will be followed as per the Schedule of Assessments.  
 
After a subject is removed or withdrawn from study treatment, the subject will be 
followed until death or withdrawal of consent for study participation, whichever 
occurs first.  
 
Off-treatment data on OS will be updated every 6 months or until death or 
withdrawal of consent for study participation, whichever occurs first. If a subject is 
removed from the study treatment due to unacceptable AE(s), the event(s) will be 
followed until resolution or stabilization of the AE(s). Subjects who respond and 
discontinue study treatment for reasons other than disease relapse should continue 
to have response assessments, and survival should be collected every 2 months until 
disease relapse, withdrawal of consent for study participation, or death, whichever 
occurs first. After disease relapse, data for survival should be collected every 6 
months until death or withdrawal of consent for study participation. 
 
Criteria for Removal from Study Treatment 
Study treatment can continue for subjects deriving clinical benefit in the opinion of 
the investigator, unless one or more withdrawal criteria are met, or at the subject’s 
discretion, or if the study is terminated. 
 
1. Study Treatment Discontinuation 
Study treatment must be discontinued if: 
• 
There is evidence of disease progression according to IWG 2006 criteria. 
(Subjects who have PD but who are continuing to derive clinical benefit in the 
opinion of the investigator may continue to receive study treatment). 
• 
A female subject becomes pregnant. 
• 
A subject is non-compliant with the requirements of the protocol.  
• 
A subject has an adverse experience that would, in the investigator’s 
judgment, make continued participation in the study an unacceptable risk. 
• 
The subject starts new treatment for their disease under study. 
• 
The subject receives HSCT. 
2. Subject Withdrawal from Study Treatment 
If the subject is permanently withdrawn from study treatment, but does not 
withdraw consent from the study, the investigator should make every effort to have 
the subject complete all withdrawal assessments at the time of withdrawal and 
complete all scheduled follow-up visits. 
 
3. Study Completion 
Subject must be taken off the study if: 
• 
The subject dies during the study. 

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• 
The subject is lost to follow-up. 
• 
The subject withdraws consent for study participation. 
 
4. Subject Withdrawal from Study 
A subject may voluntarily withdraw from study treatment or withdraw consent from 
study participation at any time. The investigator may also, at his or her discretion, 
discontinue a subject from study treatment at any time. The investigator and/or 
designated staff will record the date and the reason for subject withdrawal from the 
study. 
 
Statistics 
This is a FIH, phase 1, open-label, safety, and preliminary efficacy study of APR-548 
in combination with azacitidine in subjects with TP53-mutant MDS. 
 
The RP2D of APR-548 will be defined as the lowest of:    
1. The mBED in the monotherapy safety run-in,   
2. The dose that achieves the pre-defined level of maximum exposure in the 
monotherapy or combination therapy safety run-ins, or  
3. The dose at which there are <2 DLTs in 3-6 subjects in a cohort, in the 
monotherapy or combination therapy safety run-ins.   
 
 
The study will implement the following stopping criteria: 
 
• 
Any death within 30 days from the first dose of APR-548. 
• 
A medically equivalent SAE experienced by >1 subject within the first 30 days 
of study treatment (monotherapy and 1st cycle of combination treatment). 
• 
Any >Grade 3 AE experienced by >2 subjects within the first 30 days of study 
treatment. 
• 
Any ≥Grade 3 ocular associated AE that does not return to ≤Grade 1 or 
baseline within 7 days. 
 
If a stopping criterion is met, enrollment will be temporarily suspended until the DRT 
has performed a prompt cumulative review of safety data and the circumstances of 
the event in question, to determine whether dosing and/or the protocol should be 
modified. 
 
Determination of Sample Size 
This trial assumes a sample size of up to 46 subjects, 6 subjects in each of 6 dose 
escalation cohorts plus 10 additional subjects at the RP2D. 
 
Analysis Populations 
 
Safety population: Subjects will be evaluable for safety if they receive at least one 
dose of APR-548. The safety population will be the primary analysis population used 
for all analyses such as subject disposition, subject demographics, exposure, safety 
parameters and efficacy parameters. The safety population will be the primary 
analysis population for efficacy. 
 
Efficacy-evaluable (EE) population: All subjects who complete at least one treatment 

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cycle of APR-548 and who have at least one post-treatment clinical response 
assessment. The EE population will be the secondary analysis population for efficacy. 
 
PK population: Subjects will be evaluable for PK if at least one sample for PK 
evaluation has been obtained. 
 
Safety Analyses 
Safety data including AEs, vital signs, laboratory data, electrocardiogram (ECG), 
ophthalmologic assessment findings, and other physical exam findings will be 
tabulated for the safety population. AEs will be tabulated by System Organ Class 
(SOC), preferred term, severity, and relationship to treatments. The tabulation of 
laboratory parameters will include the normal ranges for each parameter. Each 
value will be classified as falling above, below, or within the normal range. Laboratory 
parameters will also be tabulated by maximum NCI-CTCAE v5.0 severity grade. 
 
Efficacy Analyses 
CR rate will be summarized for the safety and EE subjects as the proportion (%) of 
subjects with CR. In addition to presenting the CR rate, its associated exact 95% 
confidence intervals (CI) for each treatment arm will also be presented. 
 
DOR is defined as the time from the date when criteria for response are met to the 
date of relapse/PD or death due to any cause, whichever occurs first. Subjects alive 
with no relapse/PD will have their DOR censored at the date of the last clinical 
assessment. The DOCR will be summarized in each treatment arm by providing the 
median DOR together with associated 95% CI, using Kaplan-Meier methodology.  
 
Overall response will be summarized in number (%) of subjects in each category of 
responses (CR, PR, marrow complete response [mCR] with HI, mCR without HI, HI). 
ORR will be analyzed by using the similar method as primary endpoint CR. DOR, as 
defined above, will also be evaluated in regard to ORR. Time to AML is calculated 
from first day of study treatment to first onset of AML. Kaplan-Meier methodology 
will be utilized. Rate of AML transformation will be analyzed by using the similar 
method as primary endpoint CR. 
 
Survival data are collected at treatment and follow-up periods. Subjects will be 
followed until death or withdrawal of consent from the study, whichever occurs first.  
 
OS is defined as the number of days from the first day of treatment to the date of 
death due to any cause. Kaplan-Meier methodology will be utilized. 
 
RFS is defined as the time from the date of randomization to disease relapse or 
death, whichever occurs first. If neither event occurs, RFS will be censored at the date 
of the last clinical assessment. Kaplan-Meier methodology will be utilized. 
 
Time to AML, OS and RFS will be analyzed using the similar methods as DOR. 
 
Transition rate to HSCT will be analyzed using the similar methods as CR. 

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Pharmacokinetic Analysis 
Intense PK sampling for APR-548 and the metabolites M8 and M10 will be performed 
in the safety run-in period on Days 1, 2, 4 and 5 of monotherapy, and on Cycle 1 of 
combination therapy on Days 1, 2, 4, 5. Sparse PK sampling for APR-548 and the 
metabolites M8 and M10 will be performed in every subsequent cycle on Day 1. 
Intense PK sampling for azacitidine will be performed in Cycle 1 on Days 1, 2, 4 and 
5. 
 
PK sampling for MQ-H2O, MQ-Cys and MQ-GSH will be implemented for individual 
subjects at selected centers. Samples will be collected in the safety run-in period on 
Days 4 and 5 of monotherapy and on Cycle 1 of combination therapy on Days 4 and 
5. 
 
Non-compartmental methods will be used to derive PK parameters for APR-548, the 
metabolites and azacitidine (Cmax, Tmax, T1/2, AUC, CL/F and Vd/F, as appropriate). The 
PK of the study drugs and metabolites will be summarized using descriptive statistics 
(mean, standard deviation, CV% mean, geometric mean, CV% geometric mean). The 
concentration data for APR-548 will be evaluated using population pharmacokinetics 
(popPK) analysis in combination with data from other studies. 
 

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LIST OF ABBREVIATIONS 
Abbreviation 
Definition 
AE 
Adverse event 
AML 
Acute myeloid leukemia 
ALT 
Alanine aminotransferase 
AST 
Aspartate aminotransferase 
AUC 
Area under the curve 
BMMC 
Bone marrow mononuclear cell 
BUN 
Blood urea nitrogen 
CFR 
Code of Federal Regulations 
CHF 
Congestive heart failure 
CI 
Confidence interval 
CL 
Oral clearance 
Cmax 
Maximum concentration 
CMML 
Chronic myelomonocytic leukemia 
CNS 
Central nervous system 
CR  
Complete remission 
CRO 
Contract Research Organization 
Cys 
Cysteine 
DLT 
Dose-limiting toxicity 
DOCR 
Duration of complete remission 
DOR 
Duration of response 
DRM 
Data review meeting 
DRT 
Data Review Team 
EC 
European Commission 
ECG 
Electrocardiogram 
ECOG 
Eastern Cooperative Oncology Group 
eCRF 
Electronic Case Report Form 
EDC 
Electronic data capture 
EE 
Efficacy-evaluable 
FDA 
Food and Drug Administration 
FIH 
First-in-human 
GCP 
Good Clinical Practice  
GSH 
Glutathione 
HI 
Hematological improvement 
HMA 
Hypomethylating agent 
HSCT 
Hematopoietic stem cell transplantation 
IB 
Investigator’s Brochure 
ICH 
International Council for Harmonization 
IEC 
Independent Ethics Committee 
IPSS 
International Prognostic Scoring System 
IPSS-R 
Revised International Prognostic Scoring System 

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IRB 
Institutional Review Board 
i.v. 
Intravenous 
IWG 
International Working Group 
LFT 
Liver function test 
mBED 
Minimum biologically effective dose 
mCR 
Marrow complete response 
MDS 
Myelodysplastic syndrome 
MQ 
2-methylene-quinuclidin-3-one 
NCI-CTCAE 
National Cancer Institute Common Terminology Criteria for Adverse 
Events  
NGS 
Next-generation sequencing 
NOAEL 
No-observed-adverse-effect level 
OS 
Overall survival 
ORR 
Overall response rate 
PBMC 
Peripheral blood mononuclear cell 
PD 
Pharmacodynamic(s) 
PK 
Pharmacokinetic(s) 
p.o. 
Orally (per os) 
popPK 
Population pharmacokinetics 
PR 
Partial remission 
PRBC 
Packed red blood cells 
QD 
Once daily (quaque die) 
QTcF 
Corrected QT interval by Fridericia formula 
RBC 
Red blood cell 
RFS 
Relapse-free survival 
RP2D 
Recommended phase 2 dose 
SAE 
Serious adverse event 
s.c. 
Subcutaneous 
SCT 
stem cell transplantation 
SD-OCT 
Spectral domain optical coherence tomography 
SOC 
System Organ Class 
TEAE 
Treatment-emergent adverse event 
Tmax 
Time to maximum concentration 
TrxR1 
Thioredoxin reductase 1 
T1/2 
Half-life 
TI 
Transfusion independence 
ULN 
Upper limit of normal 
US 
United States 
USPI 
United States Prescribing Information 
VAF 
Variant allele frequency 
Vd/F 
Volume of distribution 
WHO 
World Health Organization 

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1.0 GENERAL INFORMATION 
1.1 
Protocol Number and Title of the Study 
Protocol No. A20-11202 
 
Protocol Title: Phase 1 Study to Evaluate the Safety and Efficacy of APR-548 in Combination 
with Azacitidine for the Treatment of TP53-Mutant Myelodysplastic Syndromes 
 
1.2 
Sponsor 
Aprea Therapeutics, Inc. 
 
 
 
 
 
1.3 
Medical Monitor 
 
 
 
 
1.4 
Signature Authorization 
The protocol will be signed by Aprea Therapeutics, Inc. 
 
2.0 BACKGROUND INFORMATION 
2.1 
Disease Background 
Myelodysplastic syndromes (MDS) are a heterogeneous group of neoplasms arising from a 
clonal hematopoietic precursor1,2. MDS is characterized clinically by cytopenia and a 
tendency to transform to acute myeloid leukemia (AML)3. Prognostic scoring systems have 
been developed to help stratify patients based on predicted survival and progression to 
AML3–5. In practice, treatment decisions are made by grouping patients with MDS into lower 
and higher risk subgroups as defined by clinical prognostic scoring systems. Specifically, the 
International Prognostic Scoring System (IPSS) and its more modern version, the revised-IPSS 
(IPSS-R), represent the most widely used clinical prognostic tools3,4. Those patients that fall 
in the higher risk group have an expected survival of less than 12 months if left untreated 
and progress to AML greater than 30% of the time. 
 

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2.2 
TP53 Mutations in MDS 
Patients with higher risk MDS fall into IPSS categories of intermediate-2-risk and high-risk 
groups, corresponding largely to IPSS-R groups very high, high, and, sometimes, 
intermediate. 
 
To date, the only disease modifying agents in MDS include lenalidomide in patients with 
isolated deletion of 5q (del(5q)) and the hypomethylating agents (HMA) azacitidine and 
decitabine. 
 
For higher risk MDS patients, azacitidine represents the standard of care based on the 
AZA-001 trial that demonstrated a survival advantage for azacitidine when compared with 
induction chemotherapy, low dose cytarabine, or best supportive care (24.5 months versus 
15 months, p<0.0001)6.  
 
The advent of  next-generation sequencing (NGS) has provided a rapid and efficient platform 
for genome studies that has revolutionized the diagnostic, prognostic, and therapeutic 
realms of myeloid malignancies7. Current NGS myeloid panels incorporate 20-50 genes and 
can identify mutations in the vast majority of patients8,9. In MDS, mutations of ASXL1, ETV6, 
EZH2, RUNX1 and TP53 were found to be independently associated with decreased survival10. 
Of these, recent investigations have suggested that the mutational status of TP53 is the most 
important negative prognostic factor in MDS patients. TP53 mutations are detected in up to 
20% of MDS cases, are associated with higher risk MDS, complex cytogenetics and poor 
overall survival (OS) compared to wild-type TP53 MDS.  
 
TP53 mutations are strongly associated with poor outcomes in azacitidine treated patients11. 
In addition, Bejar and colleagues recently confirmed decreased OS in TP53-mutant MDS 
patients treated with HMA without effect on response rates12. Lastly, mutations of TP53 
strongly predict for lack of benefit to allogeneic bone marrow transplantation, which 
represents the only curative option for patients with MDS13. This study highlights the 
prognostic importance of TP53 mutations as patients with complex karyotype without TP53 
mutation had similar survival to patients with normal karyotype.   
 
Overall, TP53-mutant MDS and AML patients have a median OS ranging from 5-9 months 
with 8 months representing the best estimate when restricting to MDS and oligoblastic AML 
(20-30% blasts)10,14–17. Together, these data highlight the dismal outcomes of TP53-mutant 
MDS patients and the dire need for the development of novel therapeutic strategies, 
particularly in this patient population. 
 
2.3 
APR-548 
 
 

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2.3.1 Pharmacology and Mode of Action 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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F
  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  
 
 
 
 
 
 
 
 
 
 
 
2.3.2 Pharmacokinetics  
 
 

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2.3.3 Safety Pharmacology and Toxicology 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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2.4 
Azacitidine 
Azacitidine is a nucleoside metabolic inhibitor that was approved for the treatment of 
patients with MDS of all subtypes in 2004 by the US FDA and for higher-risk MDS, chronic 
myelomonocytic leukemia (CMML) and AML with 20% to 30% blasts and multi-lineage 
dysplasia by the European Medicines Agency in 2009.  
 
Azacitidine is a pyrimidine nucleoside analogue of cytidine that exerts its antineoplastic 
activity by hypomethylation of the DNA, which has a cytotoxic effect on abnormal 
hematopoietic cells30. At low doses, azacitidine is able to induce reactivation of cell cycle-
regulating genes that were initially silenced due to hypermethylation, which may induce cell 
differentiation, reduce proliferation and/or increase apoptosis of the daughter cells31. 
 
In two early trials by Silverman et al. (CALGB 8421 and CALGB 8921)32, median duration of 
response (DOR) was 14.7 and 17.3 months for patients treated with i.v. versus subcutaneous 
(s.c.) azacitidine, respectively. In the randomized, multicenter, phase 3, CALGB 9221 trial, 
patients with MDS who received azacitidine 75 mg/m2/day s.c. for 7 days every 28 days had 
a significantly higher overall response rate (ORR) than those receiving supportive care alone 
(60% versus 5%). Hematological response data from these three trials were retrospectively 
reanalyzed using International Working Group (IWG) 2000 criteria. Among 99 patients who 
received azacitidine and 41 patients who received supportive care (without subsequently 
crossing over to azacitidine), the ORR (CR plus partial remission [PR] plus hematological 
improvement [HI]) was 47% versus 17%, with CR rates of 10% versus 0%, PR rates of 1% 
versus 0% and HI rates of 36% versus 17%33. 
 
In the randomized, open-label, multicenter, phase 3 trial AZA-001, in adults with higher-risk 
(i.e., IPSS intermediate-2-risk or high-risk classification) MDS/AML, median OS was 

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significantly better with s.c. azacitidine 75 mg/m2 per day for 7 days every 28 days than with 
conventional care (21.1 versus 11.5 months; p=0.0045) and with azacitidine versus low-dose 
cytarabine (24.5 versus 15.3 months; p=0.0006). The median time to AML transformation 
was significantly longer in patients receiving azacitidine than in those receiving conventional 
care (17.8 versus 11.5)6,34. 
 
Azacitidine is rapidly absorbed after s.c. or i.v. administration with a Vd of 76 ± 26 L and a T1/2 
of 41 ± 8 minutes. Cmax is reached after about 30 minutes. Azacitidine and its metabolites are 
known to be substantially excreted by the kidney, and the risk of adverse reactions to this 
drug may be greater in patients with impaired renal function. Urinary excretion is the 
primary route of elimination; the cumulated urinary excretion is 85% of radioactive dose with 
less than 1% recovered in feces over 3 days. 
 
Azacitidine undergoes spontaneous hydrolysis in aqueous solution and is deaminated by 
cytidine deamidases. Preliminary data indicate that drug-drug interaction with APR-548 as 
perpetrator are not likely, but the drug-drug interaction will be investigated as part of the 
current trial. 
 
2.5 
Rationale for the Starting Dose and Maximum Exposure of APR-548 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
. 
 

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2.6 
Rationale for Combination of APR-548 with Azacitidine 
 
 
. 
 
2.7 
Rationale for Dose of APR-548 in Combination with Azacitidine 
 
 
 
 
 
 
  
 
2.8 
Potential Risks and Benefits 
2.8.1 Potential Risks 
 
 
   
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  
 
 
 
 
 
 
 
 

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ions
 
 
 
 
 
 
 
 
 
 
 
 
 could be considered to originate from the CNS should 
be treated as clinically indicated. 
 
 
 
 
 
 
 
 
 
 

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2.8.2 Potential Benefits 
Patients with TP53-mutant MDS have a poor prognosis and unmet medical need. APR-548 
has demonstrated in vitro synergy with azacitidine, a standard of care agent for TP53-mutant 
MDS. The purpose of this clinical trial is to define the safety and tolerability of APR-548 in 
combination with azacitidine in patients with TP53-mutant MDS and to determine 
preliminary efficacy. Given that TP53-mutant MDS patients have a limited life expectancy and 
lack of effective treatments, the benefit/risk assessment supports the use of APR-548 in this 
trial. 
 
2.9 
Characteristics of a Well-Conducted Trial 
The following characteristics of an adequate and well-conducted trial will be implemented: 
 
1. The investigators will be well qualified by scientific training and experience. 
2. Detailed electronic eCRFs will be completed for every subject.  
3. Requirements for institutional ethics review as set forth by the appropriate IRB/IEC, 
Title 21 CFR Part 56, the European Union Directive 2001/20/EC and its associated 
Detailed Guidances, European Union GCP Directive 2005/28/EC, the ICH Guideline for 
GCP, Sections 3 and 4, and the terms of the Declaration of Helsinki (2013), will be 
followed.  
4. Requirements for informed consent in accordance with institutional guidelines, FDA 
requirements as specified in Title 21 CFR, Part 50, the European Union Directive 
2001/20/EC and its associated Detailed Guidances, European Union GCP Directive 
2005/28/EC, the ICH Guideline for GCP, Section 4.8, and the terms of the Declaration 
of Helsinki (2013), will be followed.  
5. Safety data will be recorded and evaluated.  
6. Routine monitoring visits will be conducted by the Sponsor’s representative to ensure 
data accuracy.  
7. Drug accountability will be strictly maintained.  
8. This trial will be conducted according to GCP, the protocol and applicable regulatory 
requirements. 
 

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2.10 Subject Population 
This study will enroll adult male and female subjects of age ≥18 years with documented 
diagnosis of TP53-mutant MDS, according to the World Health Organization (WHO) 
classification (<20% blasts). Subjects with relapsed/refractory TP53-mutant MDS will be 
allowed in the study. 
 
3.0 TRIAL OBJECTIVES AND PURPOSE 
3.1 
Primary Objective   
To investigate the PK, safety and tolerability of APR-548 as monotherapy and in combination 
with azacitidine and determine the recommended phase 2 dose (RP2D) of APR-548 in 
subjects with TP53-mutant MDS. 
 
3.2 
Secondary Objectives 
1. To assess preliminary clinical activity of APR-548 administered in combination with 
azacitidine.  
a. Rate of CR 
b. Duration of CR (DOCR) 
c. ORR 
d. Duration of ORR 
e. Rate of and time to development of AML transformation, as defined by WHO 
criteria 
f. OS 
g. Relapse-free survival (RFS) 
h. Rate of transition to hematopoietic stem cell transplant (HSCT) 
i. 
Rate of red blood cell (RBC) and/or platelet transfusion independence (TI) for 8 
weeks 
2. To characterize PK of APR-548 after single and multiple dosing when given orally (p.o.) 
3. To evaluate the PK drug-drug interaction between APR-548 and azacitidine. 
 
Exploratory objectives: 
 
1. To assess PD markers of APR-548 in blood and bone marrow samples. 
2. To assess molecular markers of response to APR-548 in baseline and serial blood 
samples and bone marrow samples. 
 
 

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4.0 TRIAL DESIGN 
4.1 
Overview of Trial Design 
This is an open-label FIH phase 1 clinical trial that will assess safety, PK, and clinical activity 
of p.o. administered APR-548 in combination with azacitidine for the treatment of 
TP53-mutant MDS. 
 
Treatment will be administered on an outpatient basis but may be administered in the 
inpatient setting for subjects who are hospitalized and meet criteria for study treatment. No 
investigational or commercial agents or therapies other than those described below may be 
administered with the intent to treat the subject's disease under study.  
 
The study is guided by a 3+3 dose escalation of APR-548 in the safety run-in monotherapy 
and the safety run-in combination therapy portions. 
 
APR-548 will initially be given p.o. QD during Days 1 – 4 of a 28-day safety run-in period. The 
first 3 subjects enrolled on each dose level will be evaluated for a 28-day DLT safety follow-
up period prior to enrolling additional subjects on that dose level or prior to dose escalation. 
If no DLT is observed, subjects will proceed to the safety run-in combination therapy portion 
with APR‑548 in combination with azacitidine administered s.c. or i.v. at the standard dose 
of 75 mg/m2 on Days 1-7 of the 28-day cycle. The first 3 subjects on each dose level of the 
combination with APR-548 and azacitidine will be evaluated for a 28-day DLT safety follow-
up period prior to enrolling additional subjects on that dose level or prior to dose escalation 
with the combination treatment.  
 
During the safety run-in of the monotherapy and during the safety run-in of the combination 
treatment, each subject within the dose level will be evaluated for safety and tolerability of 
APR-548. APR-548 dose escalation will be guided by an assessment of safety, PK and PD data, 
and may proceed until DLTs are observed or the pre-defined maximum exposure of APR-548 
in plasma (average Cmax and AUC 8 μM and 16 μM·h, respectively) is reached, or the minimum 
biologically effective dose (mBED) is achieved (the dose at which no further incremental 
effect on markers of apoptosis and/or proliferation is observed, in the monotherapy safety 
run-in only). The DRT, consisting of the Medical Monitor, Site Principal Investigators, retina 
specialist and other clinical research personnel that the Sponsor deems appropriate, will 
review available PK, PD and safety data for each 3-6 subject cohort in both the safety run-in 
for the monotherapy and the combination portions, and increases in dose will be guided by 
the observed safety, PK and PD data, until the RP2D is determined. The RP2D of APR‑548 will 
be defined as the lowest of: 
1. mBED in the monotherapy safety run-in, 
2. The dose that achieves the pre-defined level of maximum exposure in the 
monotherapy or combination therapy safety run-ins, or 
3. The dose at which there are <2 DLTs in 3-6 subjects in a cohort, in the monotherapy 

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or combination therapy safety run-ins.  
 
Up to 10 subjects may be enrolled at the RP2D per decision of the DRT to gain additional 
confidence in the RP2D. 
 
Subjects in Cohort 1 will receive a starting dose of 50 mg/day (Dose level 1). If there is a DLT 
in ≤1/3 subjects in Cohort 1, Cohort 1 will be expanded to enroll 3 more subjects. If ≥2 
subjects out of the total 3–6 subjects have a DLT, dose escalation will not occur. If ≤1 DLT 
occurs in the 6 subjects treated at that dose level, the subsequent subject group (Cohort 2) 
will be enrolled upon DRT review of data as described above, at the APR-548 dose of 
150 mg/day (Dose level 2). If ≥2 of 6 subjects at a dose level have a DLT, or if the pre-defined 
maximum exposure of APR‑548 in plasma is reached or the mBED is achieved (in 
monotherapy safety run-in only), then dose escalation ceases. This study will evaluate up to 
6 dose levels. Any subsequent dose escalation will not exceed 100% and will follow the same 
principle as described above. The table below shows the planned dose levels based on the 
expected APR-548 human PK and under the assumption that the doses are well tolerated. 
Once the RP2D is established, if only 3 subjects were treated at the RP2D, an additional 3 
subjects will be included in the cohort and if ≤1 DLT occurs in the 6 subjects treated at that 
dose level, the RP2D will be defined.  
 
The 
 
 
 
 
The DRT will also review any other emergent toxicities that are not explicitly defined by the 
DLT criteria to determine if any warrant a DLT designation. 

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If the dose escalation of the 28-day safety run-in proceeds more rapidly than the 
combination portion such that the dose of APR-548 undergoing evaluation in the 28-day 
safety run-in exceeds that being assessed in the combination portion, the subject will receive 
the dose of APR-548 currently being assessed for safety in the combination portion. If a 
subject in the 28-day safety run-in period has a dose reduction of APR-548 due to AE, the 
subject will proceed with Cycle 1 of the combination portion with the reduced dose of 
APR-548 in combination with standard dose azacitidine. 
 
Following discussions with the DRT, the schedule of APR-548 may be modified, including 
multiple daily and weekly doses, based on available PK, PD, and safety data. 
 
Subjects in the 28-day safety run-in period and in Cycle 1 of the combination portion who 
miss ≥25% of APR-548 doses for a nonmedical reason (e.g., subject’s preference) or 
noncompliance will be replaced. 
 
Subjects in the combination portion may receive a higher dose of APR-548 than originally 
assigned after completion of at least two cycles of combination therapy at the assigned dose 
level if safety data for a higher dose level of APR-548 in combination with azacitidine have 
been reviewed by the DRT and concluded as safe. 
 
4.1.1 Treatment Duration 
Subjects may continue treatment with APR-548 and azacitidine until disease progression, 
development of other unacceptable toxicity, confirmed pregnancy, HSCT, death, withdrawal 
of consent, or study termination, whichever occurs first. Subjects who experience disease 
progression per the applicable response criteria who are, in the opinion of the investigator, 
benefiting from treatment, may be allowed to continue on study drug with approval of the 
Medical Monitor. 
 
Following discontinuation of study drug, subjects are to attend a follow-up visit 28 days after 
the last dose of study drug for final assessments. When study drug is withheld from a subject 
in order to resolve a toxicity and the subject does not subsequently restart treatment, end 
of treatment is defined as the date when the study drug was first held. Subjects should 
proceed with end of treatment assessments, safety, and survival follow-up. If the decision to 
not restart study treatment comes outside of the 28-day safety follow-up window, the subject 
should have an End of Treatment visit and proceed with survival follow-up. 
 
Subjects who achieve an adequate response to treatment with APR-548 and meet other 
criteria required to undergo HSCT may proceed to HSCT after discontinuation of APR-548. If 
a subject proceeds to HSCT, evaluation of the extent of disease, response to treatment, and 
any new antineoplastic therapies will be collected at least monthly as long as the subject 
remains in remission and assessed as part of the study until relapse, death, withdrawal of 

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consent, loss to follow-up, or end of study, whichever comes first. If a subject discontinues 
APR-548 to undergo HSCT, but is then deemed ineligible for HSCT, the subject may restart 
APR-548 with Medical Monitor approval. 
 
All subjects that enter survival follow-up will be contacted every two months for assessment 
of survival status and new antineoplastic therapies. Please see Section 6.9 for details on long-
term follow-up. 
 
4.2 
End of Study 
The end of the study is defined as the date of the last visit of the last subject undergoing the 
trial. 
 
4.3 
Drug Products 
4.3.1 APR-548 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
4.3.2 Azacitidine 
Chemical Name:  4-amino-1--D-ribofuranosyl-s-triazin-2(1H)-one. 
 
Formulation, preparation, storage and stability: Please see commercial package insert 
approved by regulatory agencies35. 
 
Route of Administration: s.c. injection or i.v. infusion administered s.c. or i.v. for 7 consecutive 
days (Days 1-7). S.c. route is preferred but will allow for i.v. at the investigator’s discretion. 

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However, the same route should be maintained over the 7-day treatment period (whichever 
route of administration is used on Day 1, the same route should be followed on all other 
days). On the days of concomitant APR-548 administration, azacitidine will be administered 
1 hour (±15 min) after APR-548 intake. Missed doses, such as for a weekend or holiday, for 
any reason but toxicity may, at the investigator’s decision, be replaced by adding an 
additional dosing day for azacitidine so that the subject receives the total 7 days of treatment 
per cycle. If the azacitidine dose interruption is >3 days, discuss with the Medical Monitor. 
 
4.4 
Duration of Therapy 
Subjects may remain on study treatment to the end of the trial while deriving clinical benefit, 
unless unacceptable toxicity, death, or subject withdrawal. Subjects may remain on study 
treatment after disease progression if they are continuing to derive clinical benefit in the 
opinion of the investigator. 
 
4.5 
Trial Discontinuation  
The Sponsor may terminate this study prematurely. Written notification of the termination 
is required. Conditions that may warrant termination include, but are not limited to: 
 
• 
The discovery of an unexpected, significant, or unacceptable risk to the subjects enrolled 
in the study. 
• 
Failure of the investigator to enter subjects at an acceptable rate. 
• 
Insufficient adherence to protocol requirements (non-compliance). 
• 
Lack of evaluable and/or complete data. 
• 
Decision to modify the developmental plan of the drug. 
• 
A decision on the part of the Sponsor to suspend or discontinue development of the drug. 
 
The Sponsor reserves the right to discontinue the study for clinical or administrative reasons 
at any time. If the site does not recruit at a reasonable rate, the study may be discontinued 
at that site. Should the study be terminated and/or the site closed for whatever reason, all 
documentation and study drug pertaining to the study must be returned to the Sponsor or 
its representative, and the Investigators, IRB/IEC and Regulatory Authorities will be promptly 
informed of the termination and the reason for the decision. The Investigator should 
promptly inform the subjects and assure appropriate therapy and follow-up. Subjects should 
then be withdrawn from the study. 
 
4.6 
Drug Accountability/Disposition of APR-548 Supplies 
The investigator or designee will maintain accurate records of receipt and the condition of 
the study drug supplied for this study, including dates of receipt. In addition, accurate 
records will be kept of when and how much study drug is dispensed and administered to 

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each subject in the study. Any reasons for departure from the protocol dispensing regimen 
must also be recorded.  
 
At the completion of the study, there will be a final reconciliation of all study drugs.  
 
4.7 
Inclusion Criteria 
1. Provision of signed and dated, written informed consent prior to any study specific 
procedures. 
2. Documented diagnosis of TP53-mutant MDS, according to WHO criteria that is previously 
untreated and meets IPSS-R classification of intermediate, high, or very high risk disease, 
or TP53-mutant MDS that is relapsed and/or refractory to prior treatments. Eligible TP53 
mutations are defined in Appendix VII. 
3. Adequate organ function as defined by the following laboratory values: 
a. Creatinine clearance ≥60 mL/min (by Cockcroft-Gault method, Appendix I), 
b. Total serum bilirubin ≤1.5 × upper limit of normal (ULN), unless due to Gilbert’s 
syndrome or MDS organ involvement,  
c. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) ≤2.5 × ULN, 
unless due to MDS organ involvement. 
4. Age ≥18 years at the time of signing the informed consent form. 
5. Eastern Cooperative Oncology Group (ECOG) performance status of 0, 1 or 2 (Appendix 
II). 
6. Projected life expectancy of ≥12 weeks. 
7. Clear ocular media and adequate pupil dilation to permit fundus examination and retinal 
imaging. 
8. Female subjects must be surgically sterile, postmenopausal (for at least 1 year), or have 
negative results for a pregnancy test at screening, on a serum or urine sample obtained 
within 7 days prior to initiation of study treatment. 
9. Heterosexual female subjects of childbearing potential must agree to use adequate 
contraception or practice sexual abstinence as the preferred and usual lifestyle of the 
subject during the study and for up to 90 days after study treatment discontinuation. 
Adequate contraception is defined by the concomitant use of 2 effective methods of 
contraception, which can be comprised of two barrier methods, or a barrier method plus 
a hormonal method or an intrauterine device that meets <1% failure rate for protection 
from pregnancy in the product label (Appendix III). Females of non-childbearing potential 
are those who are postmenopausal greater than 1 year or who have had a bilateral tubal 
ligation or hysterectomy or bilateral oophorectomy. Female subjects must refrain from 
egg cell donation while on study treatment and for at least 90 days after the last dose of 
APR-548 or azacitidine, whichever is longer. 
10. Male subjects with female partners of childbearing potential must have had a prior 
vasectomy or agree to use an adequate method of contraception (i.e., double barrier 
method: condom plus spermicidal agent) starting with the first dose of study therapy 
through 90 days after the last dose of APR-548 or azacitidine, whichever is longer. Male 

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subjects should agree to refrain from sperm donation during the study and for at least 
90 days after the last dose of APR-548 or azacitidine, whichever is longer. Should a female 
partner of a male subject become pregnant or suspect she is pregnant while 
participating in the study, he should inform his treating physician and the female partner 
should contact her physician immediately. 
 
4.8 
Exclusion Criteria 
1. Any of the following cardiac abnormalities: 
a. Myocardial infarction within six months prior to enrollment; 
b. New York Heart Association Class III or IV heart failure (Appendix IV) or known left 
ventricular ejection fraction <40%; 
c. A history of familial long QT syndrome; 
d. Symptomatic atrial or ventricular arrhythmias not controlled by medication(s); 
e. QTcF ≥470 msec, unless due to underlying bundle branch block and/or pacemaker 
and with the approval of the Medical Monitor.  
2. Concomitant malignancies or previous malignancies with less than a 1-year disease-free 
interval at the time of signing informed consent. Subjects with adequately treated basal 
or squamous cell carcinoma of the skin, or adequately treated carcinoma in situ (e.g., 
cervix) may enroll irrespective of the time of diagnosis. Subjects with controlled, 
advanced prostate cancer are permitted. 
3. Known hypersensitivity to mannitol. 
4. Known hypersensitivity to fluorescein sodium. 
5. Use of cytotoxic chemotherapeutic agents, or experimental agents for the treatment of 
TP53-mutant MDS within 14 days or 5 half-lives of the product (whichever is shorter) of 
the first day of study drug treatment.  
6. Prior exposure to eprenetapopt (APR-246). 
7. Ongoing or prior history of ocular or hepatic graft-versus-host disease following 
allogeneic SCT. Subjects receiving systemic immunosuppressive therapy for treatment 
of 
(not 
prophylaxis) 
of 
graft-versus-host 
disease 
must 
be 
off 
systemic 
immunosuppressive therapy for a minimum of 6 weeks. 
8. A female subject who is pregnant or breast-feeding. 
9. Known history of human immunodeficiency virus, active hepatitis B or active hepatitis C 
infection. 
10. Malabsorption syndrome or other condition likely to affect gastrointestinal absorption 
of APR-548.  
11. Known history or current evidence of ocular disease in either eye that, in the opinion of 
the investigator, may confound retinal assessments (e.g., glaucoma, advanced age-
related macular degeneration, diabetic retinopathy, uveitis, or the presence of any 
condition that precludes adequate visualization of the fundus such as dense cataracts or 

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corneal scarring). 
12. Family history of Leber hereditary optic neuropathy, autosomal dominant optic atrophy, 
late-onset retinal degeneration, familial dysautonomia or other hereditary mitochondrial 
disease, unless the causative mutation(s) in the family have been determined and the 
participant has tested negative for the mutation(s). 
13. Known prior or current retinal or optic nerve disease (e.g., retinitis pigmentosa, diabetic 
retinopathy, optic neuritis) that could impact interpretation of new onset retinal or optic 
nerve disease. 
14. Corrected visual acuity worse than 20/40. 
15. Other severe acute or chronic medical or psychiatric condition or laboratory abnormality 
that, in the opinion of the investigator, may increase the risk associated with study 
participation or study treatment administration or may interfere with the interpretation 
of study results and/or would make the subject inappropriate for enrollment into this 
study. 
16. Active uncontrolled infection. 
4.9 
Inclusion of Women, Minorities and Children 
Both men and women ≥18 years of age and members of all races and ethnic groups are 
eligible for this study. Children are not eligible for this study because the safety and 
tolerability of the proposed dosing schedule has not been determined in adults. 
4.10 Withdrawal Criteria 
Protocol therapy can continue for subjects receiving clinical benefit, unless one or more 
study treatment discontinuation criteria are met, or at the subject’s discretion, or if the study 
is terminated. Subjects are free to discontinue treatment or withdraw from the study at any 
time and for any reason, without penalty to their continuing medical care. Any 
discontinuation of treatment or withdrawal from the study must be fully documented in the 
eCRF and should be followed up by the investigator. The investigator may withdraw a subject 
at any time if this is considered to be in the subject’s best interest. 
4.10.1 Study Treatment Discontinuation 
Study treatment must be discontinued if: 
• 
Evidence of disease progression according to IWG 2006 criteria. Subjects who have 
PD but who are continuing to derive clinical benefit in the opinion of the investigator 
may continue to receive study treatment. 
• 
A female subject becomes pregnant. 
• 
A subject is non-compliant with the requirements of the protocol.  
• 
A subject has an adverse experience that would, in the investigator’s judgment, make 
continued participation in the study an unacceptable risk. 
• 
The subject starts new treatment for their disease under study. 

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• 
The subject receives HSCT. 
4.10.2 Subject Withdrawal from Study Treatment 
If the subject is permanently withdrawn from study treatment, but does not withdraw 
consent from the study, the investigator should make every effort to have the subject 
complete all withdrawal assessments at the time of withdrawal and complete all scheduled 
follow-up visits. 
 
4.10.3 Study Completion 
Subject must be taken off the study if: 
• 
The subject dies during the study. 
• 
The subject is lost to follow-up. 
• 
The subject withdraws consent for study participation. 
4.10.4 Subject Withdrawal from Study 
A subject may voluntarily withdraw from study treatment or withdraw consent from study 
participation at any time. The investigator may also, at his or her discretion, discontinue a 
subject from study treatment at any time. The investigator and/or designated staff will 
record the date and the reason for subject withdrawal from the study. 
4.10.5 Withdrawn Subjects  
When a subject is removed from the study treatment, the investigator will clearly document 
the reason in the medical record and complete the appropriate eCRF page describing the 
reason for discontinuation. In addition, every effort should be made to complete the 
appropriate assessments listed in Section 6.8. 
 
Subjects who miss ≥25% of APR-548 doses for a nonmedical reason (e.g., subject’s 
preference) or noncompliance will be replaced. 
4.11 Noncompliance 
All instances of protocol deviations will be recorded according to guidelines per Sponsor’s 
representative.  
 
5.0 TREATMENT OF SUBJECTS 
5.1 
Drug Preparation and Administration 
Study treatment may be administered on an outpatient basis. No investigational or 
commercial agents or therapies other than those described below may be administered with 
the intent to treat the subject’s disease. 

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5.1.1 APR-548 
The APR-548 starting dose is 50 mg/day administered p.o during Days 1–4 for the 28-day 
safety run-in and in the 28-day cycles in the combination portion. 
 
APR-548 is distributed to sites as a powder in bottle for oral solution. APR-548 should be 
reconstituted with cold sterile water as follows: 
• 
150 mg bottle once reconstituted with 30 mL of cold sterile water will be 5 mg/mL.  
• 
150 mg bottle once reconstituted with 10 mL of cold sterile water will be 15 mg/mL.  
• 
300 mg bottle once reconstituted with 10 mL of cold sterile water will be 30 mg/mL.  
 
The prepared solution should be taken with an additional 200 mL of water at least 2 hours 
after and 1 hour before any food intake. 
 
Detailed instructions on vial concentration, preparation and dispensing can be found in the 
Pharmacy Binder. 
5.1.2 Azacitidine 
Azacitidine is given at the standard dose of 75 mg/m2 s.c. or i.v. over 7 consecutive days, Days 
1 – 7. Cycles should be repeated every 28 days. S.c. route is preferred but i.v. is allowed at 
the investigator’s discretion. The same route should be maintained over the 7-day treatment 
period (whichever route of administration is used on Day 1; the same route should be 
followed on all other days). On days of concomitant APR-548 intake, azacitidine should be 
administered 1 hour (±15 min) after APR-548. Detailed instructions on preparation and 
administration can be found in the current United States Prescribing Information (USPI)35. 
Missed doses, such as for a weekend or holiday, for any reason but toxicity may, at the 
investigator’s decision, be replaced by adding an additional dosing day for azacitidine so that 
the subject receives the total 7 days of treatment per cycle. If the azacitidine dose 
interruption is >3 days, discuss with the Medical Monitor. 
5.1.3 Dose-Limiting Toxicity 
All treatment-emergent adverse events (TEAEs) are relevant to the determination of DLTs 
unless they are clearly and solely due to the disease under study. During the 28-day safety 
run-in period for APR-548 monotherapy and during the 28-day safety run-in period for 
APR-548 in combination with azacitidine, a DLT is defined as any of the following TEAEs 
defined by the National Cancer Institute Common Terminology Criteria for Adverse Events 
(NCI-CTCAE) version 5.0, as follows:   
 
• 
Non-hematological NCI-CTCAE ≥Grade 3 AE, including ocular AEs that are different from 
retinopathy or optic nerve disorder classifications.  
• 
Prolonged myelosuppression with the persistence of ≥Grade 4 neutropenia or 
thrombocytopenia in the absence of disease lasting 14 days from the initial 

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administration of APR-548 (only during the safety run-in period for APR-548 
monotherapy). 
• 
Grade 3 nausea/vomiting/diarrhea/fatigue/CNS AE. Grade 3 nausea/vomiting/diarrhea 
may be excluded if parenteral nutrition, tube feeding, or prolonged hospitalization is 
not required. 
• 
New or worsening retinopathy or optic nerve disorder AE of any grade. 
• 
Grade 3 metabolic/electrolyte abnormalities that do not resolve to ≤Grade 1 or baseline 
within 72 hours. 
• 
Grade ≥4 neutropenia lasting past day 28 in the absence of disease. 
• 
Any AE, regardless of the NCI-CTCAE Grade, resulting in discontinuation, dose reduction 
or treatment with less than 75% of planned doses of APR-548, unless clearly and solely 
related to disease under study. 
 
Investigator should contact the Medical Monitor to discuss any findings suggestive of 
ocular-associated AEs. Any ≥Grade 2 ocular-associated AEs are considered AEs of special 
interest and should be reported as SAEs. Subjects with signs and/or symptoms of vision 
changes should be seen immediately by ophthalmologist/retinal specialist. APR-548 may be 
permanently discontinued, following a discussion with the Medical Monitor, if: 
• 
Any retinopathy or optic nerve disorder develops, regardless of perceived attribution 
to study drug, and  
• 
A clinical retina specialist or ophthalmologist determines a retinal or optic nerve 
finding is substantially changed from the subject's baseline test. 
 
Additionally, TEAEs that meet the above criteria, but occur after the DLT evaluation periods 
will not be defined as DLTs, but will be reported as AEs/SAEs and will be reviewed across all 
cohorts during the study to help determine the AE profile for the respective treatment 
regimens under study. A subject that discontinues APR-548 therapy during the DLT 
assessment period without DLT is considered evaluable for the purpose of safety only if at 
least 75% of the scheduled dose of APR-548 was administered in the monotherapy safety 
run-in period. 
 
The DRT also will review any other emergent toxicities that are not explicitly defined by the 
DLT criteria to determine if any warrant a DLT designation. 
5.1.4 Dose Escalation Strategy 
The RP2D of APR-548 will be defined as the lowest dose of APR-548 that results in:    
1. The mBED in the monotherapy safety run-in,  
2. The dose that achieves the pre-defined level of maximum exposure in the 
monotherapy or combination therapy safety run-ins, or  
3. The dose at which there are <2 DLTs in 3-6 subjects in a cohort, in the monotherapy 
or combination therapy safety run-ins.   
 

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Up to 10 subjects may be enrolled at the RP2D per decision of the DRT to gain additional 
confidence in the RP2D. 
 
DRT consisting of the Medical Monitor, Site Principal Investigators, independent retina 
specialist and other clinical research personnel that the Sponsor may deem appropriate, will 
hold data review meetings (DRMs) on an interim basis at a frequency dependent on study 
accrual. At these meetings, the DRT will review AEs and DLTs and make recommendations 
regarding the dose for the next dosing cohort and decide when the RP2D is reached. 
 
5.2 
Dose Interruptions/Withholding 
Study treatment, including APR-548 and azacitidine, may be withheld from a subject in the 
event of intercurrent illness, TEAE, administrative reasons, or other reasons. If the subject’s 
condition subsequently improves, or the situation that resulted in withholding study drug 
resolves, the investigator may resume dosing as soon as possible, unless the reason for dose 
interruption falls into one of the categories noted below. 
 
Dosing with APR-548 may be permanently discontinued in any subject who develops any 
retinopathy or optic nerve disorder (of ≥Grade 2), regardless of perceived attribution to study 
drug, and if a clinical retina specialist or ophthalmologist determines a retinal or optic nerve 
finding is substantially and clinically significantly changed from the subject’s baseline test, 
and that continued participation in the trial would increase the risk for such a finding to 
worsen (see Table 7 for details). 
 
Dose management guidelines in Table 2 or Table 3 should be followed for each occurrence 
of a ≥Grade 3 hematologic or non-hematologic toxicity where relationship to APR-548 and/or 
azacitidine cannot be excluded (e.g., due to underlying disease).  
 
Dose management guidelines in Table 4, Table 5 and Table 6, respectively, should be 
followed for each occurrence of infections, nausea/vomiting/diarrhea, and neutropenia with 
and without fever. 
 
Dose management guidelines in Table 8, Table 9 and Table 10, respectively, should be 
followed for each occurrence of CNS-associated TEAEs, renal TEAEs (serum creatinine 
elevations or acute kidney injury), or hepatic TEAEs (elevations in bilirubin, ALT and/or AST). 
 
Subjects experiencing ≥2 occurrences of the same TEAE where attribution to APR-548 and/or 
azacitidine cannot be excluded (e.g., due to underlying disease), the investigator should 
consult with the study Medical Monitor before study treatments are resumed or 
discontinued. 
 

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Treatment may be discontinued if a TEAE has not improved (≤Grade 1 or baseline level) or 
resolved after ≤4 weeks. Consult with the study Medical Monitor to discuss the subject’s 
condition before permanently discontinuing study treatment.  
 
Table 2. Dose management guidelines for new onset hematologic toxicities 
Toxicity 
Occurrence 
APR-548 
Azacitidine 
Grade 3 or 4 
hematologic 
toxicity * 
1st occurrence 
• 
Hold all study 
treatments until blood 
count(s) return to 
baseline or Grade ≤1. 
Treat promptly. 
• 
Consider reducing APR-548 
by one dose level from 
starting dose for all future 
cycles of treatment if 
toxicity does not resolve to 
Grade ≤1 within 7 days from 
onset date despite maximal 
medical intervention(s). 
 
• 
If unable to reduce APR-548 
dose, discuss with study 
Medical Monitor before 
resuming or discontinuing 
treatment. 
• 
Follow dose 
modification 
guidelines per 
USPI36.   
2nd or later occurrence 
• 
Hold all study 
treatments until blood 
count(s) return to 
baseline or Grade ≤1. 
Treat promptly. 
• 
Consult with study Medical Monitor before resuming or 
discontinuing study treatments. 
* Grade 3 and Grade 4 neutropenia with fever or Grade 4 neutropenia without fever should follow the guidelines provided 
in Table 6. 
 
Table 3. Dose management guidelines for non-hematologic toxicities 
Toxicity 
Occurrence 
APR-548 
Azacitidine 
Grade 3 or 4 
non-
hematologic 
toxicity * 
1st occurrence 
• 
Hold all study 
treatments until 
toxicity returns to 
baseline or Grade ≤ 1. 
Treat promptly.  
• 
Consider reducing APR-548 
by one dose level from 
starting dose for all future 
cycles of treatment if toxicity 
does not resolve to Grade ≤1 
within 7 days from onset date 
despite maximal medical 
intervention(s).   
 
• 
If unable to reduce APR-548 
dose, discuss with study 
Medical Monitor before 
resuming treatment. 
• 
Follow dose 
modification 
guidelines per 
USPI36.   
2nd or later occurrence 
• 
Hold all study 
treatments until 
toxicity returns to 
• 
Consult with study Medical Monitor before resuming 
study treatments. 

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baseline or Grade ≤ 1. 
Treat promptly. 
* For infections and infestation, nausea/vomiting/diarrhea, ≥ Grade 3 neutropenia, CNS-associated TEAEs, Renal TEAEs, or 
hepatic TEAEs, refer to Table 4, Table 5, Table 6, Table 8, Table 9 and Table 10, respectively for dose management guidelines.  
 
 
Table 4. APR-548 and azacitidine dose management guidelines for infection and/or 
infestation adverse events 
Toxicity 
Grade 
Occurrence 
APR-548 
Azacitidine 
Grade 3 or 4 
1st occurrence 
• 
Interrupt dosing and monitor subject; 
treat promptly.  
• 
Resume at current dose level if toxicity 
returns to baseline or Grade ≤1 in less 
than 7 days from onset date.  
• 
Reduce APR-548 by one dose level from 
starting dose for all future cycles of 
treatment if toxicity does not resolve to 
Grade ≤1 within 7 days of onset date.  
• 
If unable to reduce APR-548 dose, 
discuss with study Medical Monitor 
before 
resuming 
or 
discontinuing 
treatment. 
• 
Initiate 
or 
reassess 
infection 
prophylaxis measures. Refer to Section 
5.3.3 
for 
supportive 
management 
guidelines specific to infections or 
infestations. 
Follow dose modification 
guidelines per USPI36. 
2nd occurrence 
• 
Hold all study treatments and monitor subject; treat promptly.  
• 
Assess current infection prophylaxis measures being administered 
and adjust treatment plan as clinically indicated. Refer to Section 
5.3.3  for supportive management guidelines specific to infections 
or infestations.  
• 
While APR-548 and azacitidine are interrupted, consult with study 
Medical 
Monitor 
before 
resuming 
or 
discontinuing 
study 
treatments. 
 
 
Table 5. APR-548 dose management guidelines for nausea, vomiting, and/or 
diarrhea adverse events 
Worst toxicity grade 
Dose modification guidelines for APR-548 * 
Grade 1 
• 
Maintain dose level of APR-548 and monitor subject; provide supportive care 
measures as clinically indicated. 
Grade 2 
• 
Interrupt APR-548 dosing and monitor subject; treat promptly. 
• 
Resume at current dose level if toxicity resolves to Grade ≤1 or baseline, with or 
without use of supportive care measures, within 72 hours of onset.  
• 
If toxicity does not resolve to Grade ≤1 within 72 hours despite maximal medical 
intervention(s), then reduce APR-548 by 1 dose level once the toxicity resolves to 

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Grade ≤1 or baseline. 
• 
If unable to reduce APR-548 dose, discuss with study Medical Monitor before 
resuming or discontinuing treatment. 
• 
For subsequent doses of APR-548, pre-medication with prophylactic supportive 
therapy should be given if clinically indicated. 
Grade 3 
1st occurrence 
• 
Interrupt APR-548 dosing and monitor subject; treat promptly. 
• 
Resume at current dose level if toxicity resolves to Grade ≤1 or 
baseline, with supportive care measures, within 72 hours of 
onset.  
• 
If toxicity does not resolve to Grade ≤1 within 72 hours despite 
maximal medical intervention(s), then reduce APR-548 by 1 
dose level once the toxicity resolves to Grade ≤1 or baseline. 
• 
If unable to reduce APR-548 dose, discuss with study Medical 
Monitor before resuming or discontinuing treatment. 
• 
For subsequent doses of APR-548, pre-medication with 
prophylactic supportive therapy should be given. 
2nd occurrence 
• 
Interrupt APR-548 dosing and monitor subject; treat promptly.  
• 
Reduce APR-548 by 1 dose level if the toxicity resolves to Grade 
≤1 or baseline within 72 hours of onset. 
• 
If toxicity does not resolve to Grade ≤1 despite maximal medical 
intervention(s) within 72 hours of onset, then consult with study 
Medical Monitor before resuming or discontinuing APR-548. 
• 
If unable to reduce APR-548 dose, discuss with study Medical 
Monitor before resuming or discontinuing treatment. 
• 
Prior to subsequent doses of APR-548, reassess prophylactic 
supportive therapy regimen and adjust as clinically indicated. 
3rd occurrence 
• 
Interrupt APR-548 dosing and monitor subject; treat promptly. 
• 
Consult with study Medical Monitor before resuming or 
discontinuing APR-548. 
Grade 4 
• 
Interrupt APR-548 dosing and monitor subject; treat promptly. 
• 
Consult with study Medical Monitor before resuming or discontinuing APR-548. 
* Refer to Section 5.3.5 for details on supportive management guidelines specific to nausea, vomiting, and/or diarrhea. 
 
 
Table 6. Dose management guidelines for APR-548 and azacitidine for worsening 
neutropenia from baseline with or without fever 
Toxicity 
Occurrence 
APR-548 
Azacitidine 
Grade 3 or 4 
neutropenic 
fever 
 
or 
 
Worsening 
neutropenia 
from baseline 
to 
Grade 
4 
without fever 
1st occurrence 
• 
Interrupt dosing and monitor subject; treat 
promptly. 
• 
Resume at current dose level if neutropenia 
and fever (if present) resolve to baseline within 
7 days after onset.  
• 
If toxicity does not resolve to baseline despite 
maximal medical intervention(s) within 7 days 
of onset, then reduce  
• 
APR-548 by 1 dose level once the toxicity 
resolves to baseline. 
• 
If unable to reduce APR-548 dose, discuss with 
study Medical Monitor before resuming or 
Follow 
dose 
modification 
guidelines 
per 
USPI36. 

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discontinuing treatment. 
• 
Initiate or reassess prophylaxis measures. 
Refer to Sections 5.3.3 and 5.3.4 for supportive 
management guidelines specific to infection 
prophylaxis and neutropenia, respectively. 
2nd occurrence 
• 
Hold all study treatments and monitor subject; treat promptly. 
• 
Assess current infection prophylaxis measures being administered and 
adjust treatment plan as clinically indicated. Refer to Sections 5.3.3 and 
5.3.4 for supportive management guidelines specific to infection 
prophylaxis and neutropenia, respectively.   
• 
While APR-548 and azacitidine are interrupted, consult with study 
Medical Monitor before resuming or discontinuing study treatments. 
 
Table 7. Management of ocular-associated adverse events 
Parameter 
Worst 
toxicity  
Occurrence 
Dose Modifications for APR-548 
Retinopathy 
and optic 
nerve 
disorders 
Grade 1 
1st 
occurrence 
Interrupt treatment with APR-548. Monitor and treat patient 
promptly as clinically indicated. Consult with study medical monitor 
before resuming dosing of APR-548 at same dose level once event 
has stabilized or resolved to baseline. 
2nd 
occurrence 
Interrupt treatment with APR-548. Monitor and treat patient 
promptly as clinically indicated. Consult with study medical monitor 
to determine if patient should resume at same dose level or if APR-
548 should be reduced by 1 dose level.  
3rd 
occurrence 
Interrupt treatment with APR-548. Monitor and treat patient 
promptly as clinically indicated. Consult with study medical monitor 
to determine if APR-548 treatment should be reduced by one dose 
level or permanently discontinued. 
Grade 2 
1st 
occurrence 
Interrupt treatment with APR-548. Monitor and treat patient 
promptly as clinically indicated. 
Notify medical monitor and report as SAE (AESI).  
Once resolved to baseline parameters, then reduce dose of APR-
548 by one level. If unable to reduce dose of APR-548, discuss with 
study medical monitor before resuming or discontinuing treatment 
with APR-548. 
2nd 
occurrence 
Permanently discontinue treatment with APR-548. Monitor and 
treat patient promptly as clinically indicated. Notify medical 
monitor and report as SAE (AESI).  
≥Grade 
3 
N/A 
Permanently discontinue subject from APR-548. 
Other 
Grade 1 
 
Interrupt treatment with APR-548 for new finding or worsening from 
baseline. Monitor and treat patient promptly as clinically indicated.  
May resume at current dose level once stabilized or resolved to 
baseline. 
Consult with study medical monitor before resuming or reducing 
dose of APR-548 for a second or greater occurrence of same event. 
Grade 2 
1st 
occurrence 
Interrupt treatment with APR-548 for new finding or worsening 
from baseline. Monitor and treat patient promptly as clinically 
indicated. 
Notify Medical Monitor and report as SAE (AESI).  

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Once resolved to baseline parameters, then: 
First occurrence, reduce dose of APR-548 by one level.  If unable to 
reduce dose of APR-548, discuss with study medical monitor before 
resuming or discontinuing treatment with APR-548. 
2nd 
occurrence 
Permanently discontinue treatment with APR-548. Monitor and 
treat patient promptly as clinically indicated. Notify Medical 
Monitor and report as SAE (AESI). 
≥Grade 
3 
N/A 
Permanently discontinue subject from APR-548. 
 
Table 8. Management of CNS adverse events (e.g., dizziness, tremor, confusion, and 
ataxia) 
Worst toxicity  
Dose Modifications for APR-548 
Grade 1 
Maintain dose level 
Grade 2 
If resolved to ≤Grade 1 with medical therapy, continue same dose level 
If not resolved despite treatment interruption and maximal medical therapy, interrupt 
treatment with APR-548 and contact the study Medical Monitor. 
Grade ≥3 
Interrupt treatment with APR-548 and give medical therapy. If resolved (to ≤Grade 1) with 
medical therapy, reduce APR-548 by one dose level when treatment is restarted.   
If not resolved despite treatment interruption and maximal medical therapy, consult 
study Medical Monitor to determine if a reduction of APR-548 by one dose level could be 
undertaken once the CNS AE resolves to ≤Grade 1 or if APR-548 should be permanently 
discontinued.  
Grade 4 
Permanently discontinue subject from APR-548. 
 
 

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Table 9. Management of serum creatinine elevations and acute kidney injury 
Parameter Worst toxicity†   
Occurrence 
Dose Modifications for APR-548 
Serum 
Creatinine 
Elevations 
Grade 1 (<1.5 × 
baseline) 
N/A 
Maintain dose level of APR-548 
Grade 2 (>1.5 to 
3.0 × baseline) 
1st 
occurrence 
Omit dose until resolved to ≤Grade 1 or baseline, then 
maintain dose level. Monitor subject. 
2nd 
occurrence 
Reduce by 1 dose level. If unable to reduce by 1 dose level, 
consult with study Medical Monitor before resuming or 
discontinuing study treatment. 
Grade 3 (>3.0 – 
6.0 × baseline) 
1st 
occurrence 
Interrupt dosing with APR-548 and monitor subject. Treat 
promptly.  
Reduce by 1 dose level. If event resolved to ≤Grade 1 or 
baseline less than 7 days from onset. If unable to reduce by 
1 dose level, consult with study Medical Monitor before 
resuming or discontinuing study treatment. 
If not resolved or resolved in >7 days, evaluate if other 
contributing factors are present. If none, or after 
consideration of best interest of the subject, discontinue 
subject from APR-548.  
If other factors present, consider continuing after  1 dose 
level. 
 2nd 
occurrence 
Permanently discontinue treatment with APR-548. 
Grade 4 (>6.0 × 
baseline)  
N/A 
Permanently discontinue subject from APR-548. 
Acute 
kidney 
injury 
(including 
acute 
tubular 
necrosis) 
≤Grade 2  
1st 
occurrence 
Omit dose until resolved to ≤Grade 1 with medical therapy. 
Consult with study Medical Monitor to discuss if a dose 
reduction should be undertaken.   
 
 
2nd 
occurrence 
Permanently discontinue treatment with APR-548. 
Grade 3 
1st 
occurrence 
Omit dose until resolved to ≤Grade 1 with medical therapy. 
Consult with study Medical Monitor to determine if dose 
reduction or permanent discontinuation of APR-548 should 
be undertaken.   
2nd 
occurrence 
Permanently discontinue treatment with APR-548. 
Grade 4 
N/A 
Permanently discontinue subject from APR-548 
† Common Terminology Criteria for Adverse Events (CTCAE) version 5.  
* If dose reduction by 1 dose level is not available, consultation with study Medical Monitor should occur prior to resuming 
treatment with APR-548. 
 

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Table 10. Management of liver enzymes elevation 
Parameter 
Worst toxicity  
Occurrence 
Dose Modifications for APR-548 
Bilirubin‡ 
Grade 1 (>ULN - 
1.5 × ULN) 
N/A 
Maintain dose level with liver function tests (LFTs)≠ 
monitored as per protocol 
Grade 2 (>1.5 - 
3.0 × ULN) with 
ALT or AST ≤3.0 
× ULN 
1st occurrence 
Omit dose until resolved to ≤Grade 1 or baseline, then: 
If resolved in ≤7 days, maintain dose level. 
If resolved in >7 days, then  1 dose level. If unable to 
reduce by 1 dose level, then consult with study Medical 
Monitor before resuming or discontinuing study 
treatment. 
2nd occurrence 
Omit dose until resolved to ≤Grade 1 or baseline, then 
 1 dose level. If unable to reduce by 1 dose level, then 
consult with study Medical Monitor before resuming or 
discontinuing study treatment. 
Grade 3 (>3.0 - 
10.0 × ULN) with 
ALT or AST ≤3.0 
× ULN 
1st occurrence 
Omit dose until resolved to ≤Grade 1 or baseline, then: 
If resolved in ≤7 days,  1 dose level. If no subsequent 
event, consider re-escalation to original dose level after 
consultation with study Medical Monitor. 
Omit dose until resolved to ≤Grade 1, then:  1 dose 
level. 
If not resolved or resolved in ≤7 days, evaluate if other 
contributing factors are present. If none, or after 
consideration of best interest of the subject, 
discontinue subject from APR-548. 
2nd occurrence 
Evaluate if other contributing factors are present. If 
none, or after consideration of best interest of the 
subject, discontinue subject from APR-548.  
If other factors present, consider continuing after  1 
dose level. If unable to reduce by 1 dose level, then 
consult with study medical monitor before resuming or 
discontinuing study treatment. 
Grade 4 (>10.0 × 
ULN) 
N/A 
Permanently discontinue subject from APR-548 
AST or 
ALT 
Grade 1 (>ULN - 
3.0 × ULN if 
baseline was 
normal; 1.5 - 3.0 
× baseline if 
baseline was 
abnormal) 
N/A 
Maintain dose level with LFTs≠ monitored per protocol 
Grade 2 (>3.0 - 
5.0 × ULN if 
baseline was 
normal; >3.0 - 
5.0 × baseline if 
baseline was 
abnormal) in the 
absence of total 
bilirubin 
1st occurrence 
Omit dose until resolved to ≤Grade 1 or baseline, then, 
if resolved in ≤7 days, maintain dose level. If resolved 
in >7 days, then  1 dose level. If unable to reduce by 1 
dose level, then consult with study Medical Monitor 
before resuming or discontinuing study treatment 
2nd occurrence 
Omit dose until resolved to ≤Grade 1 or baseline, then 
 1 dose level. If unable to reduce by 1 dose level, then 
consult with study Medical Monitor before resuming or 
discontinuing study treatment. 

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Parameter 
Worst toxicity  
Occurrence 
Dose Modifications for APR-548 
elevation to > 
2.0 × ULN 
Grade 3 (>5.0 - 
20.0 × ULN if 
baseline was 
normal; >5.0 – 
20.0 x baseline if 
baseline was 
abnormal) in the 
absence of total 
bilirubin 
elevation to > 
2.0 × ULN 
1st occurrence 
Omit dose until resolved to ≤Grade 1 or baseline. 
For 1st occurrence, if resolved in ≤7 days, then maintain 
dose level. If not resolved or resolved in <7 days, 
evaluate if other contributing factors are present. If 
none, or after consideration of best interest of the 
subject, discontinue subject from APR-548. If other 
factors present, consider continuing after  1 dose 
level. If unable to reduce by 1 dose level, then consult 
with study Medical Monitor before resuming or 
discontinuing study treatment. 
2nd occurrence 
Evaluate if other contributing factors are present. If 
none, or after consideration of best interest of the 
subject, discontinue subject from APR-548. If other 
factors present, consider continuing after  1 dose 
level. If unable to reduce by 1 dose level, then consult 
with study Medical Monitor before resuming or 
discontinuing study treatment. 
Grade 4 (>20.0 × 
ULN if baseline 
was normal; 
>20.0 × baseline 
if baseline was 
abnormal) 
N/A 
Permanently discontinue subject from APR-548 
◊ Please note that the Investigator is responsible for determining whether a subject meets potential Hy’s Law criteria at any 
point during the study. Hy’s law identifies subjects at risk for severe drug-induced liver injury and is defined as AST or ALT 
≥3× ULN together with Total Bilirubin Level ≥2×ULN, where no other reason, other than the suspected drug, can be found 
to explain the combination of increases, e.g., elevated alkaline phosphatase indicating cholestasis, viral hepatitis, or another 
drug.  APR-548 should be permanently discontinued in any subject who meets potential Hy’s Law criteria.  
† Common Terminology Criteria for Adverse Events (CTCAE) version 5.  
‡ For subjects with Gilbert’s syndrome, these dose modifications apply to changes in direct bilirubin only.   
≠ LFTs include albumin, ALT, AST, total bilirubin (fractionated if total bilirubin >2.0 × ULN), alkaline phosphatase. 
 
5.3 
Supportive Management 
5.3.1 Growth Factors 
Use of hematopoietic growth factors is allowed according to institutional practice. 
 
5.3.2 Blood Products 
The use of blood products, including packed red blood cells (PRBCs) and platelet 
transfusions, are permitted and to be given at the discretion of the treating physician. 
Recommended guidelines for transfusion include a platelet threshold of 10 × 109/L for 
platelet transfusion and a hemoglobin threshold of 8.0 g/dL for PRBC transfusion or as 
clinically indicated at the discretion of treating physician.  
 

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The following recommendations were taken from National Comprehensive Cancer Network 
Guidelines for Prevention and Treatment of Cancer-Related Infections (Version 1.2021). 
 
Table 11. Recommendations for prevention and treatment of cancer-related 
infections 
Organism 
Recommendations 
Bacterial 
Consider fluoroquinolone or other suitable anti-bacterial prophylaxis during 
neutropenia 
Fungal 
Consider prophylaxis during neutropenia and for anticipated mucositis. Assess risk for 
Pneumocystis jirovecii pneumonia and select agent(s) as clinically indicated.   
Viral 
Start treatment with anti-viral medication in the setting of neutropenia and continually 
assess the risk for viral infection during treatment with anti-cancer therapy.  
 
Please refer to Section 5.4 for a description of drugs that are not allowed to be used while a 
subject is on study treatment. Refer to Section 5.2 for dose modification guidelines for APR-
548 and azacitidine therapy in the setting of severe or life-threatening infection. 
 
5.3.4 Management of Neutropenia with or without Fever 
Monitor complete blood counts at the time of study enrollment and throughout the course 
of study treatment. Supportive measures such as antimicrobials for prophylaxis or in the 
setting of prolonged myelosuppression, and/or at the first signs of infection are 
recommended to reduce the risk of a serious or severe infection that may lead to a fatal 
outcome in the setting of neutropenia with or without fever (see Section 5.3.3). Please refer 
to Section 5.4 for a description of drugs that are not allowed to be used while a subject is on 
study treatment. 
 
Myeloid growth factors may be used in the setting of severe or prolonged neutropenia (see 
Section 5.3.1). Refer to Section 5.2 for dose modification guidelines for APR-548 and 
azacitidine in the setting of severe or life-threatening neutropenia with or without the 
presence of fever.  
 

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5.3.5 Management of Nausea, Vomiting and Diarrhea 
Prior to starting study treatment, subjects should be evaluated to determine risk for nausea, 
vomiting, and/or diarrhea based on medical history and concomitant medications. 
Anti-nausea, anti-emetic, and/or anti-diarrheal medications should be initiated in subjects 
with intermediate or high risk for nausea, vomiting, or diarrhea. Subjects who experience 
nausea, vomiting, and/or diarrhea in association with APR-548 administration should be 
prescribed appropriate rescue treatment and prophylaxis (e.g., anti-nausea, anti-emetics, or 
anti-diarrheal medication). Monitor electrolyte levels and renal function during the course of 
study treatment and institute appropriate supportive care measures, such as electrolyte 
and/or fluid repletion, in the setting of vomiting and/or diarrhea. 
 
Please refer to Section 5.4 for a description of drugs that are not allowed to be used while a 
subject is on study treatment. Refer to Section 5.2 for dose modification guidelines for APR-
548 in the setting of nausea, vomiting, and/or diarrhea. 
 
 
5.3.6 Management of CNS-Related Adverse Events 
In prior APR-246 clinical studies, prochlorperazine 10 mg orally up to three times a day 
anti-emetics (e.g., ondansetron), or medication(s) to treat motion sickness (e.g., 
meclizine) have been used for prophylaxis and/or to treat CNS-related AEs that have 
occurred during treatment with APR-246. Prochlorperazine, anti-emetic, or motion sickness 
medication(s) should be administered as clinically indicated to prevent or treat CNS-related 
AEs while subjects are receiving treatment with APR-548. When prophylaxis is clinically 
indicated, it is recommended to start prochlorperazine, anti-emetic, or motion sickness 
medication(s) at least one day prior to the scheduled dose of APR-548 and continue giving 
through day 4 of each treatment cycle. Please follow dose administration guidelines in the 
current USPI for prochlorperazine, anti-emetic, or motion sickness medication(s). 
 
Refer to Table 8 for dose modification guidelines for APR-548 in the setting of CNS-related 
AEs. 
 
5.4 
Concomitant Treatment  
Subjects must not receive any other concurrent anti-cancer therapy, including investigational 
agents while on study treatment.  
 
As the metabolic pathways for APR-548 are not yet known, concomitant administration of 
strong inhibitors or inducers of cytochrome P450 isoenzymes or transporter enzymes should 
be avoided during the study. If unavoidable, the concomitant administration should be 
ceased for 2 days prior to APR-548 administration in each cycle until one day thereafter. 
 

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The use of proton pump inhibitors is prohibited for 1 week prior to APR-548 treatment until 
the day after the last APR-548 administration within a cycle. Other acid-reducing agents 
(H2-receptor antagonist and direct acting neutralizing agents) can be given up to 2 days prior 
to APR-548 administration. Then they should be stopped until the day after APR-548 
administration within each cycle. If needed, direct acting neutralizing agents can be given on 
the APR-548 treatments days starting 4 hours after administration until bedtime. No acid 
reducing agents should be taken in the morning prior to APR-548 intake. 
 
As the mechanism of action for APR-548 is associated with enhanced oxidative stress in 
tumor cells, use of the following medications that may antagonize therapeutic effects of 
APR-548 is discouraged, but not prohibited during study treatment administration:  
 
• 
Antioxidants (including but not limited to coenzyme Q10) 
• 
Supplementation with vitamin C, vitamin E, zinc and/or selenium outside of a daily multi-
vitamin 
• 
Iron chelators (e.g., deferoxamine or deferasirox) 
• 
Melatonin 
 
Investigator should contact the Medical Monitor to discuss the subject’s concomitant 
treatment, if the subject is taking one or more of the medications listed above or plans to 
start taking any of these medications while on study treatment. 
 
Subjects may continue their baseline medications as long as they are not prohibited. 
Palliative and supportive care (e.g., anti-emetics, bisphosphonates) for disease-related 
symptoms may be utilized as clinically indicated. AEs will be treated as clinically indicated. All 
concomitant medications should be recorded in the eCRF. 
 
5.5 
Monitoring Subject Compliance 
This study will be monitored by Aprea Therapeutics, Inc. or its Contract Research 
Organization (CRO) according to ICH E6 guidelines of GCP. The study site monitor will 
regularly visit the study sites to ensure that the study is conducted according to the protocol 
and GCP principles. All instances of protocol deviations will be entered and reviewed by the 
investigator, Sponsor and appropriate
  
 
6.0 STUDY EVALUATIONS 
6.1 
Schedule of Study Assessments 
Study assessments are summarized in Table 12 and described in Sections 6.2 through 6.9. 

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Table 12. Schedule of assessments  
Assessments 
Screening a 
Safety Run-In (APR-548 Monotherapy) b 
APR-548 + Azacitidine Combination 
End of 
treat-
ment x 
Long-
term 
follow-
up y 
Cycle 1 (Safety Run-In) 
Cycle 2 
Cycles 3+ 
D1 
D2 
D3 
D4 
D
5 
D
8 
D 
15 
D
21 
D
28 
D1  
D2 
- 7 
D8 
D15 
D 
22 
D1 c 
D2 
- 7 
D8 
D15 
 
D1d 
D2-
7 
D15
e 
Informed consent 
× 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Mutant TP53 confirmation f 
× 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical history g 
× 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Physical examination h 
× 
× 
 
 
 
 
 
× 
× 
 
× 
 
 
× 
× 
× 
 
 
 
× 
 
 
× 
 
Vital signs h 
× 
× 
× 
× 
× 
 
 
× 
× 
 
× 
× 
 
× 
× 
× 
× 
 
 
× 
× 
 
× 
 
Height i 
× 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Weight 
× 
× 
 
 
 
 
 
× 
× 
 
× 
 
 
× 
× 
× 
 
 
 
× 
 
 
× 
 
ECOG performance status 
× 
× 
 
 
 
 
 
× 
× 
 
× 
 
 
× 
× 
× 
 
 
 
× 
 
 
× 
 
APR-548 j 
 
× 
× 
× 
× 
 
 
 
 
 
×j 
× 
 
 
 
×j 
× 
 
 
× 
× 
 
 
 
Azacitidine k 
 
 
 
 
 
 
 
 
 
 
× 
×  
 
 
 
× 
×  
 
 
× 
× 
 
 
    
Disease assessment l 
× 
 
 
 
 
 
 
× 
 
 
 
 
 
 
 
 
 
 
 
× 
 
 
× 
 
Hematology m 
× 
× 
 
 
 
 
× 
 
× 
 
× 
 
× 
× 
 
× 
 
× 
× 
× 
 
× 
× 
 
Serum chemistry n 
× 
× 
 
 
 
 
× 
 
× 
 
× 
 
× 
× 
 
× 
 
× 
× 
× 
 
× 
× 
 
Creatinine clearance o 
× 
× 
 
 
 
 
× 
 
× 
 
× 
 
× 
× 
 
× 
 
× 
× 
× 
 
× 
× 
 
Coagulation profile p 
× 
 
 
 
 
 
 
 
 
 
× 
 
 
 
 
× 
 
 
 
 
 
 
 
 
Pregnancy test q 
× 
 
 
 
 
 
 
 
 
 
× 
 
 
 
 
× 
 
 
 
× 
 
 
× 
 
ECG r 
× 
× 
× 
 
× 
× 
 
 
 
 
× 
× 
 
 
 
× 
 
 
 
× 
 
 
× 
 
APR-548 PK sample s 
 
× 
× 
  
× 
× 
 
 
 
 
× 
× 
 
 
 
× 
 
 
 
× 
 
 
 
 
Azacitidine PK sample s 
 
 
 
 
 
 
 
 
 
 
× 
× 
 
 
 
 
 
 
 
 
 
 
 
 
PBMC/BMMC sample 
collection t 
× 
 
 
 
 
 
 
× 
 
 
 
 
 
 
 
 
 
 
 
× 
 
 
× 
 
Blood sample for PD 
markers u 
 
× 
× 
 
× 
× 
 
 
 
 
× 
× 
 
 
 
 
 
 
 
 
 
 
 
 
Bone marrow biopsy 
(optional) 
 
 
 
 
× 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Ophthalmological evaluation v 
× 
 
 
 
 
 
 
× 
 
× 
 
 
 
× 
 
× 
 
 
× 
× 
 
×v 
× 
 
Clinical safety assessment w 
 
Starting at the time of study treatment initiation through 30 days after last dose 
 
Concomitant medications 
Reviewed throughout study 
 
Transfusion log 
From 8 weeks prior to enrollment to end of treatment/off treatment 
 
Survival 
 
× 

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Footnotes to schedule of assessments 
 
a. All screening/baseline assessments are performed within 28 days prior to the start of study 
treatment. In the event that a visit or test cannot be scheduled on the exact visit day, a window of 
±3 days is allowable. 
b. A window of ±1 day is allowable for visits during the safety run-in (APR-548 monotherapy) period.  
c. A window of ±2 days is allowable for this visit. 
d. After the first cycle, Day 1 assessments of subsequent cycles are to be done within 3 days prior to 
next cycle drug administration. 
e. A window of ±5 days is allowable for this visit. 
f. 
Can be confirmed using archived sample. 
g. Full medical history is obtained at screening for safety and eligibility purposes; this will include any 
clinically significant findings from 28 days prior to screening date. 
h. Physical exam and vital signs (including blood pressure, heart rate, respiration rate and 
temperature) are completed for safety purposes and clinically significant items are recorded as 
AEs where appropriate. Vital signs are collected on days of APR-548 administration. 
i. 
Can be recorded historically from up to 1 year prior to informed consent. 
j. 
APR-548 is administered p.o. on Days 1–4 of each 28-day cycle. Cycle 1 Day 1 of the combination 
treatment may proceed following ophthalmic evaluation performed by retina specialist to ensure 
there are no retinal or optic nerve associated AEs, and to evaluate for other potential ocular AEs. 
k. Azacitidine is administered s.c. or i.v. over 7 consecutive days, on Days 1-7 of each 28-day cycle. 
SC route is preferred but may be given i.v. at the investigator’s discretion. The same route should 
be maintained over the 7-day treatment period (whichever route of administration is used on Day 
1; the same route should be followed on all other days). 
l. 
Subjects will have the extent of their disease assessed based on IWG 2006 criteria (Appendix V). 
Bone marrow aspirates and core sampling should be performed according to standard of care 
and analyzed at the local site’s laboratory in accordance with the International Council for 
Standardization in Hematology (ICSH) Guidelines37. Disease assessment is performed at 
screening, based on peripheral blood and/or bone marrow according to standard of care. 
Optional disease assessment may be performed during monotherapy safety run-in at 
approximately Day 15 at the discretion of the investigator. Starting on Cycle 3 Day 1 (±7 days) 
disease assessment will be performed every two cycles (every 8 weeks), through Month 12. 
Thereafter, evaluation of disease response, including bone marrow and peripheral blood, will be 
conducted every three cycles (every 12 weeks) during treatment, independent of dose delays 
and/or dose interruptions, and/or at any time when progression of disease is suspected. Samples 
for exploratory endpoints are collected at each disease assessment timepoint. 
m. Hematology must include complete blood count with white blood cell differential. Results of 
hematology parameters have to be reviewed prior to initiation of each treatment cycle.  

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n. Serum chemistry must include sodium, potassium, chloride, magnesium, CO2, blood urea nitrogen 
(BUN), creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase. Results of serum chemistry parameters have to be reviewed prior to initiation of 
each treatment cycle. 
o. Calculated using Cockcroft-Gault method (Appendix I). 
p. Coagulation profile will include prothrombin time or INR, and activated partial thromboplastin 
time. 
q. Serum or urine βhCG must be performed within 7 days prior to study treatment initiation in 
female subjects of childbearing potential. 
r. 
Standard 12-lead ECGs in triplicate at screening, on Days 1, 2, 4 and 5 of the safety run-in period, 
and on Days 1, 2, 4 and 5 of Cycle 1 and on Day 1 of each subsequent cycle with subject in a semi-
recumbent position prior to APR-548 administration. Please consult Table 15 for ECG collection 
schedule. 
s. See Section 7.3 for PK collection schedule.  
t. 
Peripheral blood/bone marrow (or both; whichever sample is collected for disease assessment) 
mononuclear cells collection for exploratory biomarker testing. Disease assessment on 
approximately Day 15 during the monotherapy safety-run in is optional. 
u. Blood sample for PD markers, collected pre-dose, 8 hours post dose, and 24 hours post dose on 
Day 1 and 4 of the safety run-in and Cycle 1. The 24 h post-dose timepoints correspond to pre-
dose Day 2 and Day 5, respectively 
v. Please consult Section 7.6 for the schedule of ophthalmological evaluation. 
w. AE description, grade, start date, resolution date, outcome, and relationship to study treatment 
should be documented. For the time period from signing of informed consent up to receipt of the 
first dose of APR-548, non-serious events should be recorded as medical history on the 
appropriate eCRF page within the clinical database. SAE(s) that occur during the screening period 
are required to be reported and should include an assessment on whether the SAE was related to 
a protocol-defined procedure or activity. 
x. Visit conducted at 28 days after study treatment discontinuation. A window of ±14 days is 
allowable for End of Treatment ophthalmological evaluation. 
y. Long-term follow-up can be done remotely (e.g., via telephone, via local practitioner or via review 
of medical records). All subjects who undergo HSCT following discontinuation of APR-548 are to 
be followed after the last dose until relapse or end of study. Subjects who respond and 
discontinue study treatment for reasons other than disease relapse should continue to have 
response assessments, and survival should be collected every 2 months until disease relapse, 
withdrawal of consent for study participation, or death, whichever occurs first. After disease 
relapse, data for survival should be collected every 6 months until death or withdrawal of consent 
for study participation. If a subject proceeds to HSCT, evaluation of the extent of disease, response 
to treatment, and any new antineoplastic therapies will be collected at least monthly as long as 
the subject remains in remission and assessed as part of the study until relapse, death, withdrawal 

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of consent, lost to follow-up, or end of study, whichever comes first. If a subject is removed from 
the study due to unacceptable AEs, the event(s) will be followed until resolution or stabilization of 
the AE. 

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6.2 
Pre-Study Assessments 
Prior to performing any procedures or assessments, the nature of the study and the 
potential risks associated with the trial will be explained to all subject candidates and written 
informed consent will be obtained. Subjects who choose to participate will have to consent 
to collection and storage of blood for correlative studies. Evaluations obtained as part of 
routine medical care and performed during the screening period may be used in place of the 
study specific evaluations. Subjects will acknowledge and agree to the possible use of this 
information for the study by giving informed consent. 
 
6.3 
Screening 
All screening evaluations are to be performed within approximately 28 days of study 
treatment initiation, unless otherwise noted. 
• 
Signed written informed consent  
• 
Mutant TP53 confirmation 
• 
Medical history  
• 
Physical examination 
• 
Height: historical record can be used from up to 1 year in the past 
• 
Weight  
• 
ECOG performance status (Appendix II) 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
Hematology, including complete blood count with white blood cell differential 
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Coagulation profile 
• 
Serum or urine βhCG must be performed within 7 days prior to study treatment 
initiation for female subjects of childbearing potential 
• 
ECG: standard 12-lead ECGs with subject in a semi-recumbent position in triplicate 
• 
Blood and bone marrow for exploratory biomarker sample testing 
• 
Concomitant medication review 
• 
Baseline disease assessment (bone marrow aspirates and core sampling, within 28 
days of study treatment initiation) 
• 
Baseline ophthalmologic evaluation, per Table 16 
• 
Transfusion log 
 
6.4 
Safety Run-In Period (APR-548 Monotherapy) 
6.4.1 Day 1 
• 
Physical examination 

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• 
Weight 
• 
ECOG performance status (Appendix II) 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
Hematology, including complete blood count with white blood cell differential 
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
• 
APR-548 administration 
• 
Blood sampling for APR-548 PK, per Table 13 
• 
Blood sampling for PD markers (pre-dose, and 8 hours post-dose)  
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.4.2 Days 2 – 4 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
APR-548 administration 
• 
Blood sampling for APR-548 PK, per Table 13 
• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
(Days 2 and 4) 
• 
Optional bone marrow biopsy (Day 4) for correlative analyses 
• 
Blood sampling for PD markers (Day 2: 24 hours post Day 1 dose, Day 4: pre-dose and 
8 hours post dose) 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.4.3 Day 5 
• 
Blood sampling for APR-548 PK, per Table 13 
• 
Blood sampling for PD markers (Day 5: 24 hours post Day 4 dose) 
• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.4.4 Day 8 
• 
Hematology, including complete blood count with white blood cell differential  

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• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.4.5 Day 15 
• 
Physical examination 
• 
Weight 
• 
ECOG performance status (Appendix II) 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
Optional disease assessment per IWG 2006 criteria (Appendix V) 
• 
Blood and bone marrow for exploratory biomarker sample testing 
• 
Ophthalmologic evaluation, per Table 16 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.4.6 Day 21 
• 
Physical examination 
• 
Weight 
• 
ECOG performance status (Appendix II) 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
Hematology, including complete blood count with white blood cell differential 
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.4.7 Day 28 
• 
Ophthalmologic evaluation, per Table 16 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 

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6.5 
Cycle 1 (APR-548 + Azacitidine Safety Run-In Period) 
6.5.1 Day 1 
• 
Physical examination 
• 
Weight 
• 
ECOG performance status (Appendix II) 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
Hematology, including complete blood count with white blood cell differential 
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Coagulation profile 
• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
• 
APR-548 administration 
• 
Azacitidine administration. Azacitidine is administered 1 hour (±15 min) after APR-548 
• 
Blood sampling for APR-548 and azacitidine PK, per Table 13 
• 
Blood sampling for PD markers (pre-dose, and 8 hours post-dose)  
• 
Serum or urine βhCG for female subjects of childbearing potential 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.5.2 Days 2 – 4 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
APR-548 administration 
• 
Azacitidine administration. Azacitidine is administered 1 hour (±15 min) after APR-548 
• 
Blood sampling for APR-548 and azacitidine PK, per Table 13 
• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
(Days 2 and 4) 
• 
Blood sampling for PD markers (Day 2: 24 hours post-dose; Day 4: pre-dose, and 8 
hours post-dose)  
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.5.3 Days 5 – 7 
• 
Azacitidine administration 
• 
Blood sampling for APR-548 and azacitidine PK, per Table 13 (Day 5) 

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• 
Blood sampling for PD markers (Day 5; 24 hours post Day 4 dose) 
• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
(Day 5) 
• 
Blood sampling for PD markers (Day 5; 24 hours post-dose)  
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.5.4 Day 8 
• 
Hematology, including complete blood count with white blood cell differential  
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.5.5 Day 15 
• 
Physical examination 
• 
Weight 
• 
ECOG performance status (Appendix II) 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
Hematology, including complete blood count with white blood cell differential  
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Ophthalmologic evaluation, per Table 16 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.5.6 Day 22 
• 
Physical examination 
• 
Weight 
• 
ECOG performance status (Appendix II) 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
Clinical safety assessment 
• 
Concomitant medications review 

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• 
Transfusion log 
 
 
6.6 
Cycle 2 
6.6.1 Day 1 
• 
Physical examination 
• 
Weight 
• 
ECOG performance status (Appendix II) 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
Hematology, including complete blood count with white blood cell differential  
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Coagulation profile 
• 
APR-548 administration. Cycle 1 Day 1 treatment may proceed following 
ophthalmologic evaluation performed by retina specialist to ensure there are no 
clinically significant ocular-associated AE 
• 
Azacitidine administration on Days 1-7. Azacitidine is administered 1 hour (±15 min) 
after APR-548 
• 
Blood sampling for APR-548 and azacitidine PK, per Table 13 
• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
• 
Serum or urine βhCG for female subjects of childbearing potential 
• 
Ophthalmologic evaluation, per Table 16 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.6.2 Days 2 – 7 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
APR-548 administration on Days 2-4 
• 
Azacitidine administration on Days 2-7. On the days of concomitant administration, 
azacitidine is administered 1 hour (±15 min) after APR-548 
• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
(Days 2 – 4) 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 

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6.6.3 Day 8 
• 
Hematology, including complete blood count with white blood cell differential  
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.6.4 Day 15  
• 
Hematology, including complete blood count with white blood cell differential  
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Ophthalmologic assessment: complete ophthalmic exam, spectral domain optical 
coherence 
tomography 
(SD-OCT), 
color 
fundus 
photography, 
fundus 
autofluorescence and fluorescein angiography 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
 
6.7 
Cycle 3 and Onwards 
6.7.1 Day 1 
• 
Physical examination 
• 
Weight 
• 
ECOG performance status (Appendix II) 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature 
• 
Hematology, including complete blood count with white blood cell differential 
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Disease assessment per IWG 2006 criteria (Appendix V). Disease assessment is 
performed every two cycles (every 8 weeks) through Month 12, based on peripheral 
blood and/or bone marrow according to standard of care. Thereafter, disease 
assessment will be conducted every three cycles (every 12 weeks). 

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• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
• 
APR-548 administration 
• 
Blood sampling for APR-548 and azacitidine PK, per Table 13 
• 
Azacitidine administration over 7 consecutive days, on Days 1-7. S.c. route is preferred 
but may be given i.v. at the investigator’s discretion. The same route should be 
maintained over the 7-day treatment period (whichever route of administration is 
used on Day 1, the same route should be followed on all other days). 
• 
Blood and bone marrow for exploratory biomarker sample testing 
• 
Serum or urine βhCG for female subjects of childbearing potential 
• 
Ophthalmologic evaluation, per Table 16 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.7.2 Days 2 – 7 
• 
Vital signs, including blood pressure, heart rate, respiration rate and temperature  
• 
APR-548 administration on Days 2-4 
• 
Azacitidine administration on Days 2-7. On the days of concomitant administration, 
azacitidine is administered 1 hour after APR-548 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.7.3 Day 15  
• 
Hematology, including complete blood count with white blood cell differential  
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Ophthalmologic evaluation, per Table 16 (only in Cycle 3) 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.8 
End of Treatment Visit 
This visit should take place within 28 days of the last dose of study treatment, if treatment is 
stopped early for any reasons.   
 
• 
Physical examination 
• 
Weight  

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• 
Vital signs 
• 
ECOG performance status (Appendix II) 
• 
Hematology, including complete blood count with white blood cell differential 
• 
Serum chemistry, including sodium, potassium, chloride, magnesium, CO2, BUN, 
creatinine, glucose, calcium, albumin, total protein, total bilirubin, AST, ALT, alkaline 
phosphatase 
• 
Creatinine clearance (Cockcroft-Gault method; Appendix I) 
• 
Disease assessment per IWG 2006 criteria (Appendix V) 
• 
Blood and bone marrow for exploratory biomarker sample testing 
• 
Ophthalmologic evaluation per Table 16 
• 
ECG: standard 12-lead ECG with subject in a semi-recumbent position, per Table 15 
• 
Serum or urine βhCG 
• 
Clinical safety assessment 
• 
Concomitant medications review 
• 
Transfusion log 
 
6.9 
Long-Term Follow-Up 
Long-term follow-up can be done remotely (e.g., via telephone, via local practitioner or via 
review of medical records). All subjects who undergo HSCT following discontinuation of 
APR-548 are to be followed after the last dose until relapse or end of study. Subjects who 
respond and discontinue study treatment for reasons other than disease relapse should 
continue to have response assessments, and survival should be collected every 2 months 
until disease relapse, withdrawal of consent for study participation, or death, whichever 
occurs first. After disease relapse, data for survival should be collected every 6 months until 
death or withdrawal of consent for study participation. If a subject proceeds to HSCT, 
evaluation of the extent of disease, response to treatment, and any new antineoplastic 
therapies will be collected at least monthly as long as the subject remains in remission and 
assessed as part of the study until relapse, death, withdrawal of consent, lost to follow-up, 
or end of study, whichever comes first. If a subject is removed from the study due to 
unacceptable AEs, the event(s) will be followed until resolution or stabilization. 
 
 
7.0 STUDY ASSESSMENTS 
7.1 
Safety Assessments 
7.1.1 Safety Analysis 
Safety data will be tabulated for all subjects and include vital signs, laboratory parameters, 
ECG and AEs. 
 

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7.1.2 Reporting of Adverse Events 
7.1.2.1 Adverse Events 
An AE is any untoward medical occurrence in a subject administered a pharmaceutical 
product that does not necessarily have a causal relationship with the treatment. An AE can 
be any unfavorable and unintended sign (including a laboratory finding), symptom or disease 
temporally associated with the use of a medicinal (investigational) product, whether or not 
related to the medicinal (investigational) product.  
 
The AE reporting period starts at the time of study treatment initiation. At each evaluation, 
subjects should be interviewed in a non-directed manner to elicit potential adverse reactions 
from the subject. The occurrence of an AE will be based on changes in the subject’s physical 
examination, laboratory results, and/or signs and symptoms. 
 
For the time period from signing of informed consent up to receipt of the first dose of 
APR-548, non-serious events should be recorded as medical history on the appropriate eCRF 
page within the clinical database. SAEs that occur during the screening period are required 
to be reported and should include an assessment on whether the SAE was related to a 
protocol-defined procedure or activity. 
 
All AEs (except laboratory abnormalities that are assessed as not clinically significant by the 
investigator, or examining ophthalmologist as applicable), regardless of causal relationship, 
are to be recorded in the eCRF and source documentation. The investigator must determine 
the intensity of any AEs according to the NCI-CTCAE version 5.0 and their causal relationship 
to each study medication administered that has been administered to the subject at the time 
of event onset. Those AEs not covered by these criteria will be graded as follows:  
 
1. 
Mild: Discomfort noticed, but no disruption of normal daily activity. Prescription drug 
not ordinarily needed for relief of symptom but may be given because of personality 
of subject. 
2. 
Moderate: Discomfort sufficient to reduce or affect normal daily activity. Subject is 
able to continue in study; treatment for symptom may be needed. 
3. 
Severe: Incapacitating, severe discomfort with inability to work or to perform normal 
daily activity. Severity may cause cessation of treatment with test drug; treatment for 
symptom may be given and/or subject hospitalized. 
4. 
Life-Threatening: Symptom(s) place the subject at immediate risk of death from the 
reaction as it occurred; it does not include a reaction that, had it occurred in a more 
serious from, might have caused death. 
5.  
Fatal: Event caused the death of the subject.  
 
AEs will be followed until resolution or stabilization while the subject remains on-study. Once 
the subject is removed from study, events thought to be related to the study medication will 

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be followed until resolution or stabilization, unless, in the investigator’s opinion the event is 
unlikely to resolve due to the subject’s underlying disease, or until the subject starts a new 
treatment regimen or the subject is lost to follow-up. 
 
The end of the AE and SAE reporting period is 30 days after last dose of study treatment, 
unless the subject has withdrawn consent for study participation or started new therapy for 
underlying disease. Progression of primary disease should be reported on a response 
assessment eCRF in this FIH study. Events unequivocally related only to progression of 
primary disease do not need to be reported separately on the AE CRF page. Hospitalization 
to start new therapy for primary disease after confirmed progression/relapse does not meet 
reporting criteria for an AE or SAE. 
 
7.1.2.2 AE Relationship Attribution Definitions 
An AE is considered to be associated with the use of the study treatment if the attribution is 
determined as possible or definite.  
 
The relationship of each AE to study treatment should be evaluated by the Investigator using 
the following criteria:  
 
• 
Definitely related: A clinical event, including laboratory test abnormality, occurring in 
a plausible time relationship to the medication administration, and which cannot be 
explained by concurrent disease or other drugs or chemicals. The response to 
withdrawal of the drug should be clinically plausible.  
• 
Possibly related: A clinical event, including laboratory test abnormality, with a 
reasonable time sequence to the medication administration, but which could also be 
explained by concurrent disease or other drugs or chemicals. Information on the drug 
withdrawal may be lacking or unclear.  
• 
Unlikely related: A clinical event, including laboratory test abnormality, with little or 
no temporal relationship to medication administration, and which other drugs, 
chemicals, or underlying disease provide plausible explanations.  
• 
Not related: A clinical event, including laboratory test abnormality that has no 
temporal relationship to the medication or has more likely alternative etiology. 
 
7.1.2.3 Definition of an Unexpected Adverse Event 
An unexpected AE is defined as any adverse drug experience, the specificity or severity of 
which is not consistent with the reference safety information in the current Investigator’s 
Brochure (IB) for a study product or products administered to a subject; or, if an IB is not 
available, the specificity or severity of which is not consistent with the risk information 
described in this protocol or in the regulatory agency study authorization application.  
 

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For study treatments used in this protocol that have been approved for use in the US by the 
FDA (i.e., azacitidine), the reference safety information that will be used for making 
expectedness decisions is the most current version of the product USPI that can be found 
on the FDA website.   
 
Unexpected, as used in this definition, refers to an adverse drug experience that has not 
been previously observed (e.g., included in the IB or other product reference safety 
information such as the USPI) rather than from the perspective of such experience not being 
anticipated from the pharmacological properties of the pharmaceutical product. 
 
7.1.2.4 Serious Adverse Event 
An SAE is defined as any untoward medical occurrence that at any dose: 
 
1. 
Results in death, 
2. 
Is life-threatening (i.e., the subject was at risk of death at the time of the event. It does 
not refer to an event which hypothetically might have caused death if it was more 
severe), 
3. 
Requires inpatient hospitalization or prolongation of existing hospitalization 
excluding that for pain management, disease staging/re-staging procedures, or 
catheter placement unless associated with other serious events, 
4. 
Results in persistent or significant disability/incapacity, or 
5. 
Is a congenital anomaly/birth defect. 
 
Important medical events that may not result in death, be life-threatening, or require 
hospitalization may be considered serious adverse drug events when, based on appropriate 
medical judgment, they may jeopardize the subject and may require medical or surgical 
intervention to prevent one of the outcomes listed above. 
 
7.1.2.5 Pregnancy 
Any pregnancy detected during the study, or that occurs within 30 days after stopping study 
medication, must be reported immediately to the investigator. Pregnancy, in and of itself, is 
not regarded as an AE, unless there is suspicion that study medication may have interfered 
with the effectiveness of a contraceptive medication. If the subject becomes pregnant while 
on-study, the study drug should be immediately discontinued. Pregnancy information about 
a female subject or a female partner of a male subject should be reported immediately from 
the time the investigator first becomes aware of a pregnancy or its outcome. This will be 
performed by the investigator per instructions from the Sponsor’s monitoring CRO.  
 
Any pregnancy complication, spontaneous abortion, elective termination of a pregnancy for 
medical reasons, outcome of stillbirth, congenital anomaly/birth defect, or SAE in the mother 
will be recorded as an SAE and will be reported as described in Section 7.1.2.6.  

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7.1.2.6 Reporting of Serious Adverse Events 
AEs classified as serious require expeditious handling and reporting to Sponsor’s monitoring 
CRO to comply with regulatory requirements. 
 
For any SAE that occurs while a subject is on-study; within 30 days of the last study treatment 
administration, regardless of any opinion as to the relationship of the SAE to the study 
treatment; or if any SAE that the investigator feels is related to the study treatment occurs 
later than 30 days after the last study treatment administration, 
Safety 
Desk must be notified immediately (within 24 hours of becoming aware of the event). The 
primary mechanism for reporting an SAE to the sponsor will be the electronic data collection 
tool. An SAE eCRF should be completed in the electronic data capture (EDC) system within 24 
hours of site becoming aware of the event. EDC Alerts will be sent to Safety desk for all SAEs. 
  
If the EDC system is inaccessible/unavailable, then the site will use the paper SAE form in 
order to report the SAE within 24 hours. Emailing the paper SAE forms is the preferred 
method of notification.           
 
SAEs will be reported to: 
Email: 
 
 
 
7.1.2.7 Safety Monitoring Plan  
The Medical Monitor is responsible for ongoing safety monitoring for the study per the 
detailed safety plan. This monitoring will include a review of all SAEs as they are reported by 
the study site. The Medical Monitor will also be in contact with site monitors and will be 
available to discuss any issues concerning safety with site staff. Safety data will be reviewed 
periodically by
 and the Sponsor Medical Officer. 
 
DRT consisting of the Medical Monitor, Site Principal Investigators, independent retina 
specialist and other clinical research personnel that the Sponsor may deem appropriate, will 
hold DRMs on an interim basis at a frequency dependent on study accrual. At these 
meetings, the DRT will review AEs, DLTs and other safety data as applicable and make 
recommendations regarding dose escalation and the RP2D. 
 
The DRT will produce summaries or minutes of these meetings. These summaries will be 
available for inspection when requested by any of the regulatory bodies charged with the 
safety of human subjects and the integrity of data. 
 

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7.2 
Efficacy Assessments 
7.2.1 Complete Remission Rate  
CR rate will be summarized for the safety and efficacy-evaluable (EE) subjects as the 
proportion (%) of subjects with CR per the IWG 2006 criteria (Appendix V)38. In addition to 
presenting the CR rate, its associated exact 95% CI will also be presented. 
 
7.2.2 Duration of Response 
DOR is defined as the time from the date when criteria for response are met to the date of 
PD or death due to any cause, whichever occurs first. Subjects alive with no PD will have their 
DOR censored at the date of the last clinical assessment. The DOCR will be summarized by 
providing the median DOR together with associated 95% CI, using Kaplan-Meier 
methodology.  
 
7.2.3 Overall Response 
Overall response will be summarized in number (%) of subjects in each category of responses 
(CR, PR, marrow complete response [mCR] with HI, mCR without HI, HI). ORR will be analyzed 
by using the similar method as primary endpoint CR. DOR, as defined above, will also be 
evaluated in regard to ORR. Time to AML is calculated from first day of study treatment to 
first onset of AML. Kaplan-Meier methodology will be utilized. Rate of AML transformation 
will be analyzed by using the similar method as primary endpoint CR. 
7.2.4 Overall Survival 
Survival data are collected at treatment and follow-up periods. Subjects will be followed until 
death or withdrawal of consent from the study, whichever occurs first.  
 
OS is defined as the number of days from the first day of treatment to the date of death due 
to any cause. Kaplan-Meier methodology will be utilized. 
 
7.2.5 Relapse-Free Survival 
RFS is defined as the time from the date of randomization to disease relapse or death, 
whichever occurs first. If neither event occurs, RFS will be censored at the date of the last 
clinical assessment. Kaplan-Meier methodology will be utilized. 
 
7.2.6 Rate of AML Transformation, Transition to HSCT, and Transfusion Independence 
Rate of AML transformation, transition rate to HSCT, and rate of RBC TI and/or platelet TI will 
be analyzed using the similar methodology as CR rate. 
 

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7.3 
Pharmacokinetics  
Whole blood concentrations of APR-548 will be measured in the safety run-in period and in 
Cycle 1 of the combination portion, at the timepoints provided in Table 13. Plasma samples 
from Cycle 1 for analysis of azacitidine will be taken as indicated in Table 13. 
 
Table 13. PK blood sampling timepoints for APR-548 and azacitidine in the safety run-
in period and subsequent cycles 
Period 
Day 
Time relative to APR-548 dose (h) 
 Pre-
dose 
 
0.25 
a 
 0.5 a 
 0.75 
a 
 1 b 
 1.5 b 
2 b 
4 b 
6 b 
8 b 
Safety Run-In  
(APR-548 
monotherapy) 
1 
× 
× 
× 
× 
× 
× 
× 
× 
× 
× 
2 
× 
 
  
 
  
 
  
 
 
 
4 
× 
× 
× 
× 
× 
× 
× 
× 
× 
× 
5 
× 
 
 
 
 
 
 
 
 
 
Cycle 1 
(APR-548 + 
Azacitidine) 
1 
× 
× 
× 
× 
×c,d 
× 
×d 
×d 
×d 
×d 
2 
×d 
 
  
 
  
 
  
 
 
 
4 
× 
× 
× 
× 
×c,d 
× 
×d 
×d 
×d 
×d 
5 
×d 
 
 
 
 
 
 
 
 
 
Subsequent 
cycles 
1 
× 
 
 
 
× 
 
× 
 
 
 
a. 
A window of ±5 minutes is allowable for this collection. 
b. 
A window of ±15 minutes is allowable for this collection. 
c. 
Cycle 1 of combination therapy. Whole blood sample for APR-548 analysis and plasma sample for azacitidine analysis 
directly prior to azacitidine administration. 
d. 
Cycle 1 of combination therapy. Plasma samples for azacitidine administration to be taken at the same time as whole 
blood samples for APR-548. 
The PK sampling timepoints (0.25, 0.75, 1.5 hours post dose) can be reduced once the Cmax and T1/2 are established. The 
Sponsor will provide a written memo to sites, which should be submitted to IRBs and can be implemented per local site 
requirements. 
 
 
PK blood sample for the measurements of whole blood concentrations of the unstable MQ 
adducts MQ-H2O, MQ-Cys and MQ-GSH will be implemented at selected centers which are 
equipped to conduct the critical sampling handling procedures described in the lab manual. 
All subjects enrolled in these centers will participate in this assessment and it is anticipated 
that data from at least 6 subjects will be available. The PK sampling schedule is provided in 
Table 14.  
 

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Table 14. PK blood sampling timepoints for MQ-H2O, MQ-Cys and MQ-GSH for 
subjects at selected centers 
Period 
Day 
Time relative to APR-548 dose (h) 
 Pre-
dose 
0.25 
a 
 0.5 a 
 0.75 
a 
 1 b 
 1.5 b 
2 b 
4 b 
6 b 
8 b 
Safety Run-In  
(APR-548 
monotherapy) 
4 
× 
× 
× 
× 
× 
× 
× 
× 
× 
× 
5 
× 
 
 
 
 
 
 
 
 
 
Cycle 1 
(APR-548 + 
Azacitidine) 
4 
× 
× 
× 
× 
× 
× 
× 
× 
× 
× 
5 
× 
 
 
 
 
 
 
 
 
 
a. 
A window of ±5 minutes is allowable for this collection. 
b. 
A window of ±15 minutes is allowable for this collection. 
The PK sampling timepoints (0.25, 0.75, 1.5 hours post dose) can be reduced once the Cmax and T1/2 are established. The 
Sponsor will provide a written memo to sites, which should be submitted to IRBs and can be implemented per local site 
requirements. 
 
 
7.4 
Pharmacodynamics  
Blood samples for PD biomarkers are collected pre-dose, 8 hours post dose, and 24 hours 
post dose on Day 1 and Day 4 in safety run-in and Cycle 1 (the 24 h post-dose timepoints 
correspond to pre-dose Day 2 and Day 5, respectively). Flow cytometry analysis will be 
completed by central laboratory. 
 
Peripheral blood/bone marrow (whichever sample is collected for disease response 
assessment) mononuclear cells collection for exploratory biomarker sample testing, 
including DNA mutation panel, RNA expression profile, TP53 VAF by NGS, will be done at each 
response assessment. Descriptive statistics will be written. Not all listed analyses may be 
performed. 
 

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7.5 
Electrocardiographic Assessment 
Table 15 describes the routine ECG requirements. 
Table 15. ECG assessment requirements 
Time Point 
ECG, 
number 
Timing 
Screening 
Triplicate 
Within 28 days of study treatment 
Safety Run-In, Day 1 
Triplicate 
Pre-dose; 0.5, 1, 2, 3 and 4 hours after APR-548 
administration (±10 min) 
Safety Run-In, Day 2 
Triplicate 
Pre-dose 
Safety Run-In, Day 4 
Triplicate 
Pre-dose; 0.5, 1, 2, 3 and 4 hours after APR-548 
administration (±10 min) 
Safety Run-In, Day 5 
Triplicate 
Pre-dose 
Cycle 1, Day 1 
Triplicate 
Pre-dose; 0.5, 1, 2, 3 and 4 hours after APR-548 
administration (±10 min) 
Cycle 1, Day 2 
Triplicate 
Pre-dose 
Cycle 1, Day 4 
Triplicate 
Pre-dose; 0.5, 1, 2, 3 and 4 hours after APR-548 
administration (±10 min) 
Cycle 1, Day 5 
Triplicate 
Pre-dose 
Cycles 2+, Day 1 
Triplicate 
Pre-dose, 1- and 2-hours post dose (±10 min) 
End of Treatment 
Triplicate 
- 
 
Schedule of ECG assessments may be modified upon Sponsor notification, based on 
available data. 
The following ECG parameters are to be captured in eCRF: heart rate, PR interval, RR interval, 
QT interval and QT interval corrected for heart rate using Fridericia's formula: QTc=QT/RR1/3. 
If a subject starts treatment with a medication known to prolong QT interval at any time 
during the study treatment period, an additional pre- and post-dose (4 hours after APR-548 
administration, ±10 min) ECG should be performed on the next APR-548 treatment day 
unless such pre- and post-dose ECGs are already required on that next APR-548 treatment 
day per the schedule of study assessments. 
 

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7.6 
Ophthalmological Evaluation 
Table 16 describes the schedule of ophthalmological evaluation. 
Table 16. Ophthalmological evaluation 
Assessments a 
Screen-
ing b, c 
Safety Run-In d 
Cycle 1 (1st 
combination 
cycle) 
Cycle 2 & 3  
 
Subse-
quent 
Cycles 
 
End of 
treatm
ent i  
D15 e 
D28 e 
D15 e 
 D1 f 
D15 f 
D1 f 
Complete ophthalmic exam 
b 
× 
× 
× 
× 
× 
× 
× 
× 
Visual field test g 
× 
× 
 
× 
× 
× 
× 
× 
SD-OCT h 
× 
× 
× 
× 
× 
× 
× 
× 
Color fundus photography 
× 
× 
× 
× 
× 
× 
× 
× 
Fundus autofluorescence 
× 
× 
 
× 
× 
× 
× 
× 
Fluorescein angiography 
× 
 
 
× 
× 
× 
 
 
a. 
All evaluations are to be performed prior to administration of a next scheduled dose. 
b. 
Complete ophthalmic exam includes best corrected distance visual acuity utilizing Early Treatment Diabetic Retinopathy 
Study (ETDRS) scale, intraocular pressure measurement using Tono-Pen or Goldmann (the same modality should be 
used throughout the study), slit lamp exam (anterior and posterior segments), dilated fundus (using indirect 
ophthalmoscopy). Additional testing may be performed at discretion of the retina specialist. Applicable ophthalmologic 
assessment may be repeated at an unscheduled visit during the study if clinically indicated. An ophthalmic CRF is 
completed by the examining retina specialist at each visit. 
c. 
Performed within 14 days of initial APR-548 administration. 
d. 
Applies to the 28-day safety run-in period for APR-548 monotherapy and the 28-day safety run-in period for APR-548 in 
combination with azacitidine. 
e. 
A window of ±4 days is allowable for this visit. This visit has to be completed prior to Cycle 1 Day 1 (1st combination cycle). 
f. 
A window of ±5 days is allowable for this visit. 
g. 
An automated, threshold perimetry with Humphrey visual field analyzer using 30-2 testing protocol. 
h. 
Spectral domain optical coherence tomography of the macula and optic nerve, including ganglion cell complex analysis 
with study-specified and standard data acquisition algorithms utilized. 
i. 
Visit conducted at 28 days (±14 days) after study treatment discontinuation. 
Please consult the A20-11202 study ophthalmic reference manual and ocular assessment 
worksheets for details. Ocular assessment worksheets are to be completed by retina 
specialist and submitted to the site for each visit. 
 
 
8.0 STATISTICS 
Demographic data and disease-related characteristics will be summarized using descriptive 
statistics (count and percent, mean, median, standard deviation, minimum, maximum). 
Continuous variables will be presented by n, mean, median, standard deviation and range 
(minimum and maximum), and categorical variables will be presented by count and 
percentage of subjects as appropriate. Data will be presented by each dose level in safety 
lead-in dose-finding portion and in the expansion portion. All subject data, efficacy and 
safety data will be summarized.   
 

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8.1 
Sample Size 
This trial assumes a sample size of up to 46. 
 
8.2 
Analysis Populations 
Safety population: Subjects will be evaluable for safety if they receive at least one dose of 
APR-548. The safety population will be the primary analysis population used for all analyses 
such as subject disposition, subject demographics, exposure, safety parameters and efficacy 
parameters. The safety population will be the primary analysis population for efficacy. 
 
EE population: All subjects who complete at least one treatment cycle of APR-548 and who 
have at least one post-treatment clinical response assessment. The EE population will be the 
secondary analysis population for efficacy. 
 
PK population: Subjects will be evaluable for PK if at least one sample for PK evaluation has 
been obtained. 
 
8.3 
Endpoints 
8.3.1 Primary 
1. Occurrence of DLTs, classified and graded according to the NCI-CTCAE version 5.0 
2. Frequency of TEAEs and SAEs related to APR-548 alone and in combination with 
azacitidine 
3. RP2D of APR-548 
 
8.3.2 Secondary  
1. Rate of CR 
2. DOCR, defined as the time from documentation of CR to disease relapse 
3. DOR, defined as the time from documentation of tumor response to disease 
relapse/progression or death as a result of any cause 
4. ORR is the proportion of subjects achieving HI, PR, CR, marrow CR by modified IWG 
2006 criteria 
5. Rate of and time to AML transformation, according to WHO criteria 
6. OS 
7. RFS 
8. Proportion of subjects who transition to HSCT 
9. Subjects who achieve RBC and/or platelet TI during the 8-week period after 
enrollment 
10. PK parameters: Cmax, Tmax, AUC, oral Vd/F, oral clearance (CL/F) and elimination T1/2 of 
APR-548 in the absence and presence of azacitidine. 

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11. PK parameters: Cmax, Tmax, AUC, T1/2 of APR-548 and the metabolites M8 (reduced 
MQ-glutathione adduct), M10 (reduced MQ-cysteine adducts), MQ water adducts 
(MQ-H2O) and MQ glutathione adducts (MG-GSH). 
 
8.3.3 Exploratory 
1. PD markers of APR-548 may be explored using flow cytometry and molecular 
techniques including, but not limited to, markers of apoptosis and proliferation 
2. Exploratory analyses of molecular markers of response may include: TP53 VAF by 
NGS, mutations and VAF of other genes by NGS, and gene and protein expression 
 
8.4 
Safety Stopping Criteria 
The study will implement the following stopping criteria: 
 
• 
Any death within 30 days from the first dose of APR-548. 
• 
A medically equivalent serious AE experienced by >1 subject within the first 30 days 
of study treatment (monotherapy and 1st cycle of combination treatment). 
• 
Any > Grade 3 AE experienced by >2 subjects within the first 30 days of study 
treatment. 
• 
Any ≥ Grade 3 ocular associated AE that does not return to ≤ Grade 1 or baseline 
within 7 days. 
 
If a stopping criterion is met, enrollment will be temporarily suspended until the DRT has 
performed a prompt cumulative review of safety data and the circumstances of the event in 
question, to determine whether dosing and/or the protocol should be modified. 
 
8.5 
Safety 
Safety data including AEs, vital signs, laboratory data, ECG, ophthalmologic assessment 
findings, and other physical exam findings will be summarized for the safety population. AEs 
will be tabulated by system organ class (SOC), preferred term, severity, and relationship to 
treatments. The tabulation of laboratory parameters will include the normal ranges for each 
parameter. AE terms will be coded using the Medical Dictionary for Drug Regulatory 
Activities, version 22.1 or higher. AEs will be summarized by SOC, preferred term, severity, 
and relationship to treatment. SAEs, deaths, and AEs leading to APR-548 dose modifications 
including interruptions, reductions, and early discontinuation of study treatment will be 
summarized. Laboratory parameters will be summarized by maximum NCI-CTCAE version 
5.0 severity grade and also by change from pre-treatment to scheduled time points using 
descriptive statistics. Laboratory parameter listings will include the normal ranges for each 
parameter. Each value will be classified as falling above, below, or within the normal range.  
 

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AEs are to be collected from the time of first dose of APR-548 and SAEs are to be collected 
from the time of signing informed consent, throughout study enrollment, and up to 30 days 
after last dose of APR-548 or azacitidine, whichever is later. Data summaries will include only 
TEAEs, defined as events occurring at the first administration of APR-548 up to and including 
30 days after last dose of study treatment. 
 
8.6 
Efficacy 
CR rate will be summarized for the safety and EE subjects as the proportion (%) of subjects 
with CR. In addition to presenting the CR rate, its associated exact 95% CI for each treatment 
arm will also be presented. 
 
 
DOR is defined as the time from the date when criteria for response are met to the date of 
PD or death due to any cause, whichever occurs first. Subjects alive with no PD will have their 
DOR censored at the date of the last clinical assessment. The DOCR will be summarized in 
each treatment arm by providing the median DOR together with associated 95% CI, using 
Kaplan-Meier methodology.  
 
Overall response will be summarized in number (%) of subjects in each category of responses 
(CR, PR, mCR with HI, mCR without HI, HI). ORR will be analyzed by using the similar method 
as primary endpoint CR. DOR, as defined above, will also be evaluated in regard to ORR. Time 
to AML is calculated from first day of study treatment to first onset of AML. Kaplan-Meier 
methodology will be utilized. Rate of AML transformation will be analyzed by using the similar 
method as primary endpoint CR. 
Survival data are collected at treatment and follow-up periods. Subjects will be followed until 
death or withdrawal of consent from the study, whichever occurs first.  
 
OS is defined as the number of days from the first day of treatment to the date of death due 
to any cause. Kaplan-Meier methodology will be utilized. 
 
RFS is defined as the time from the date of randomization to disease relapse or death, 
whichever occurs first. If neither event occurs, RFS will be censored at the date of the last 
clinical assessment. Kaplan-Meier methodology will be utilized. 
 
Time to AML, OS and RFS will be analyzed using the similar methods as DOR. 
 
Transition rate to HSCT will be analyzed using the similar methods as CR. 
 
8.7 
Pharmacokinetic Analysis 
Intense PK sampling for APR-548 and the metabolites M8 and M10 will be performed in the 
safety run-in period on Days 1, 2, 4 and 5 of monotherapy, and on Cycle 1 of combination 
therapy on Days 1, 2, 4, 5. Sparse PK sampling for APR-548 and the metabolites M8 and M10 

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will be performed in every subsequent cycle on Day 1. Intense PK sampling for azacitidine 
will be performed in Cycle 1 on Days 1, 2, 4 and 5. 
 
PK sampling for MQ-H2O, MQ-Cys and MQ-GSH will be implemented for individual subjects 
at selected centers. Samples will be collected in the safety run-in period on Days 4 and 5 of 
monotherapy and on Cycle 1 of combination therapy on Days 4 and 5. 
 
Non-compartmental methods will be used to derive PK parameters for APR-548, the 
metabolites and azacitidine (Cmax, Tmax, T1/2, AUC, CL/F and Vd/F). The PK of the study drugs 
and metabolites will be summarized using descriptive statistics (mean, standard deviation, 
CV% mean, geometric mean, CV% geometric mean). The concentration data for APR-548 will 
be evaluated using popPK analysis in combination with data from other studies. 
 
During the dose escalation part of the safety run-in and Cycle 1 of the combination 
treatment, PK analysis of APR-548 and its metabolites will be conducted on an ongoing basis 
to allow review of the PK data prior to the dose escalation decision. Prediction of APR-548 
for human PK will be updated on an ongoing basis to ensure that the exposure levels at the 
next dosing cohort do not exceed the pre-specified average maximum levels. Furthermore, 
PK variability will also be taken into account to ensure that the exposure levels in an 
individuum will not exceed the pre-specified individual maximum levels. Exploratory 
exposure/safety analysis will be conducted on an ongoing basis for APR-548 and the 
metabolites to detect any relationship of safety signals with exposure levels and to guide the 
dose selection for the next cohort. If additional preclinical data indicate that more 
differentiated safety margins should be applied for one or more APR-548 metabolites, the 
protocol will be amended accordingly. 
 
8.8 
Exploratory analyses 
Descriptive statistics/results from exploratory analyses will be written. Results for PD 
biomarkers will include marker changes in different blood cell populations; results for 
response prediction and monitoring may include but are not limited to TP53 VAF by NGS, 
mutations in other genes by NGS, RNA expression. 
 
 
9.0 QUALITY CONTROL AND QUALITY ASSURANCE PROCEDURES 
9.1 
Monitoring of the Study and Regulatory Compliance 
The project manager, or designee, will make an initiation site visit to each institution to 
review the protocol and its requirements with the investigator(s), inspect the drug storage 
area, fully inform the investigator of his/her responsibilities and the procedures for assuring 
adequate and correct documentation. During the initiation site visit the eCRFs will be 
reviewed. Other pertinent study materials will also be reviewed with the investigator’s 

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research staff. During the course of the study, the monitor will make regular site visits in 
order to review protocol compliance, examine eCRFs and individual subject’s medical records 
and assure that the study is being conducted according to pertinent regulatory 
requirements. All eCRF entries will be verified with source documentation. The review of 
medical records will be done in a manner to assure that subject confidentiality is maintained.  
 
9.2 
Curricula Vitae and Financial Disclosure of Investigators  
All Principal Investigators will be required to provide a current signed and dated curriculum 
vitae, a completed FDA Form 1572 and a financial disclosure statement to Sponsor’s 
monitoring CRO. All Sub-Investigators will be required to provide a current curriculum vitae 
and a financial disclosure statement to Sponsor’s monitoring CRO. 
 
9.3 
Protocol Modifications 
No modification of the protocol should be implemented without the prior written approval 
of the Sponsor or the Sponsor’s representative. Any such changes which may affect a 
subject’s treatment or informed consent, especially those increasing potential risks, must 
receive prior approval by the IRB/IEC. The exception to this is where modifications are 
necessary to eliminate an immediate hazard to trial subjects, or when the change involves 
only logistical or administrative aspects of the trial (e.g., change in monitor, change in 
telephone number). Other administrative revisions which may impact the clinical portion of 
a study will be duly reported to the IRB/IEC by the Principal Investigator. 
 
9.4 
Publication Policy 
The publication of the results of the study will be subject to the terms and conditions of the 
clinical trial agreement between the Sponsor and Investigators. Sponsor approval is required 
for publication of any data from this trial.  
 
 
10.0 ETHICAL CONSIDERATIONS 
10.1 Informed Consent 
The investigator will obtain written informed consent from each subject, or their authorized 
representative, participating in the study. The form must be signed, witnessed, and dated. 
The informed consent form will contain all the Essential Elements of Informed Consent set 
forth in 21 CFR, Part 50, the European Union Directive 2001/20/EC and its associated Detailed 
Guidances, European Union GCP Directive 2005/28/EC, the ICH Guideline for GCP, 
Section 4.8, and the terms of the Declaration of Helsinki (2013). Copies of the signed 
document should be given to the subject and filed in the investigator’s study file, as well as 
the subject’s medical record if in conformance with the institution’s Standard Operating 
Procedures.  

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10.2 Institutional Review Board/Independent Ethics Committee 
The study will not be initiated without approval of the appropriate IRB/IEC and compliance 
with all administrative requirements of the governing body of the institution. This protocol, 
consent procedures, and any amendments must be approved by the IRB/IEC in compliance 
with current regulations of the FDA and the European Union as applicable and in accordance 
with ICH/GCPs. A letter of approval will be sent to the Sponsor prior to initiation of the study 
and when any subsequent modifications are made. The IRB/IEC will be kept informed by the 
investigator, Sponsor’s monitoring CRO or the Sponsor, as required by national regulations, 
as to the progress of the study as well as to any serious and unexpected AEs.  
 
10.3 Subject Privacy  
In order to maintain subject confidentiality, all eCRFs, study reports and communications 
relating to the study will identify subjects by initials and assigned subject numbers; subjects 
should not be identified by name. In accordance with local, national or federal regulations, 
the investigator will allow the Sponsor or designee personnel access to all pertinent medical 
records in order to verify the data gathered on the eCRFs and to audit the data collection 
process. Regulatory agencies such as the US FDA may also request access to all study 
records, including source documentation for inspection. Clinical information will not be 
released without the written permission of the subject as outlined in the subject consent 
form. 
 
 
11.0 DATA HANDLING AND RECORDKEEPING 
11.1 Data to be Entered Directly in the Case Report Form 
The eCRF will be the source record. 
 
11.2 Recording of Data 
Data collected during the study will be entered in the subject’s eCRF by the investigational 
site staff. The staff will keep records of the subject’s visit in the files considered as source 
documents for the site, e.g., hospital chart, research chart. The investigator will be 
responsible for the recording of all data on the eCRF and for submitting the data to the 
Sponsor or their designee in a timely manner. Should any value be significantly different 
from normal, the investigator will comment in the appropriate sections provided in the eCRF.  
 
The investigator will provide access to his/her original records to permit a representative 
from the Sponsor to verify the proper transcription of data.  
 

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11.3 Study Records 
U.S. Federal laws require that an investigator maintain all study records for the indication 
under investigation for two years following the date a Product Licensing Application is 
approved or, if no application is to be filed or if the application is not approved for such 
indication, until two years after the investigation is discontinued and the FDA is notified. 
 
 

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12.0 REFERENCES 
1.  
Greenberg PL. Myelodysplastic syndromes. Clinical practice guidelines in oncology. J 
Natl Compr Canc Netw. 2003;1(4):456-471. 
2.  
Cazzola M, Della Porta MG, Malcovati L. The genetic basis of myelodysplasia and its 
clinical relevance. Blood. 2013;122(25):4021-4034. doi:10.1182/blood-2013-09-381665 
3.  
Greenberg PL, Tuechler H, Schanz J, et al. Revised international prognostic scoring 
system for myelodysplastic syndromes. Blood. 2012;120(12):2454-2465. 
doi:10.1182/blood-2012-03-420489 
4.  
Greenberg P, Cox C, LeBeau MM, et al. International scoring system for evaluating 
prognosis in myelodysplastic syndromes. Blood. 1997;89(6):2079-2088. 
doi:10.1182/blood.v89.6.2079 
5.  
Kantarjian H, O’Brien S, Ravandi F, et al. Proposal for a new risk model in 
myelodysplastic syndrome that accounts for events not considered in the original 
International Prognostic Scoring System. Cancer. 2008;113(6):1351-1361. 
doi:10.1002/cncr.23697 
6.  
Fenaux P, Mufti GJ, Hellstrom-Lindberg E, et al. Efficacy of azacitidine compared with 
that of conventional care regimens in the treatment of higher-risk myelodysplastic 
syndromes: a randomised, open-label, phase III study. Lancet Oncol. 2009;10(3):223-
232. doi:10.1016/S1470-2045(09)70003-8 
7.  
Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated 
high-density picolitre reactors. Nature. 2005;437(7057):376-380. 
doi:10.1038/nature03959 
8.  
Malcovati L, Hellström-Lindberg E, Bowen D, et al. Diagnosis and treatment of 
primary myelodysplastic syndromes in adults: Recommendations from the European 
LeukemiaNet. Blood. 2013;122(17):2943-2964. doi:10.1182/blood-2013-03-492884 
9.  
Papaemmanuil E, Gerstung M, Malcovati L, et al. Clinical and biological implications 
of driver mutations in myelodysplastic syndromes. Blood. 2013;122(22):3616-3627. 
doi:10.1182/blood-2013-08-518886 
10.  
Bejar R, Stevenson K, Abdel-Wahab O, et al. Clinical Effect of Point Mutations in 
Myelodysplastic Syndromes. N Engl J Med. 2011;364(26):2496-2506. 
doi:10.1056/NEJMoa1013343 
11.  
Bally C, Adès L, Renneville A, et al. Prognostic value of TP53 gene mutations in 
myelodysplastic syndromes and acute myeloid leukemia treated with azacitidine. 
Leuk Res. 2014;38(7):751-755. doi:10.1016/j.leukres.2014.03.012 

Aprea Therapeutics, Inc. 
Protocol Number A20-11202 
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10 September 2021 
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12.  
Bejar R, Lord A, Stevenson K, et al. TET2 mutations predict response to 
hypomethylating agents in myelodysplastic syndrome patients. Blood. 
2014;124(17):2705-2712. doi:10.1182/blood-2014-06-582809 
13.  
Bejar R, Stevenson KE, Caughey B, et al. Somatic mutations predict poor outcome in 
patients with myelodysplastic syndrome after hematopoietic stem-cell 
transplantation. J Clin Oncol. 2014;32(25):2691-2698. doi:10.1200/JCO.2013.52.3381 
14.  
Sallman DA, Komrokji R, Vaupel C, et al. Impact of TP53 mutation variant allele 
frequency on phenotype and outcomes in myelodysplastic syndromes. Leukemia. 
2016;30(3):666-673. doi:10.1038/leu.2015.304 
15.  
Desoutter J, Gay J, Berthon C, et al. Molecular prognostic factors in acute myeloid 
leukemia receiving first-line therapy with azacitidine. Leukemia. 2016;30(6):1416-
1418. doi:10.1038/leu.2015.314 
16.  
Haase D, Stevenson KE, Neuberg D, et al. TP53 mutation status divides 
myelodysplastic syndromes with complex karyotypes into distinct prognostic 
subgroups. Leukemia. 2019;33(7):1747-1758. doi:10.1038/s41375-018-0351-2 
17.  
Hou HA, Chou WC, Kuo YY, et al. TP53 mutations in de novo acute myeloid leukemia 
patients: Longitudinal follow-ups show the mutation is stable during disease 
evolution. Blood Cancer J. 2015;5(7):e331. doi:10.1038/bcj.2015.59 
18.  
Wiman KG. Pharmacological reactivation of mutant p53: From protein structure to 
the cancer patient. Oncogene. 2010;29(30):4245-4252. doi:10.1038/onc.2010.188 
19.  
Sallman DA, DeZern AE, Garcia-Manero G, et al. Eprenetapopt (APR-246) and 
Azacitidine in TP53-Mutant Myelodysplastic Syndromes. J Clin Oncol. January 
2021:JCO2002341. doi:10.1200/JCO.20.02341 
20.  
Cluzeau T, Sebert M, Rahmé R, et al. Eprenetapopt Plus Azacitidine in TP53-Mutated 
Myelodysplastic Syndromes and Acute Myeloid Leukemia: A Phase II Study by the 
Groupe Francophone des Myélodysplasies (GFM). J Clin Oncol. February 
2021:JCO2002342. doi:10.1200/JCO.20.02342 
21.  
Wiman KG. Strategies for therapeutic targeting of the p53 pathway in cancer. Cell 
Death Differ. 2006;13(6):921-926. doi:10.1038/sj.cdd.4401921 
22.  
Lambert JMR, Gorzov P, Veprintsev DB, et al. PRIMA-1 Reactivates Mutant p53 by 
Covalent Binding to the Core Domain. Cancer Cell. 2009;15(5):376-388. 
doi:10.1016/j.ccr.2009.03.003 
23.  
Tessoulin B, Descamps G, Moreau P, et al. PRIMA-1Met induces myeloma cell death 
independent of p53 by impairing the GSH/ROS balance. Blood. 2014;124(10):1626-

Aprea Therapeutics, Inc. 
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1636. doi:10.1182/blood-2014-01-548800 
24.  
Peng X, Zhang MQZ, Conserva F, et al. APR-246/PRIMA-1MET inhibits thioredoxin 
reductase 1 and converts the enzyme to a dedicated NADPH oxidase. Cell Death Dis. 
2013;4(10):e881. doi:10.1038/cddis.2013.417 
25.  
Poet GJ, Oka OB, Lith M, et al.  Cytosolic thioredoxin reductase 1 is required for 
correct disulfide formation in the ER . EMBO J. 2017;36(5):693-702. 
doi:10.15252/embj.201695336 
26.  
Lambert JMR, Moshfegh A, Hainaut P, Wiman KG, Bykov VJN. Mutant p53 reactivation 
by PRIMA-1 MET induces multiple signaling pathways converging on apoptosis. 
Oncogene. 2010;29(9):1329-1338. doi:10.1038/onc.2009.425 
27.  
Mohell N, Alfredsson J, Fransson Å, et al. APR-246 overcomes resistance to cisplatin 
and doxorubicin in ovarian cancer cells. Cell Death Dis. 2015;6(6):e1794-e1794. 
doi:10.1038/cddis.2015.143 
28.  
Haffo L, Lu J, Bykov VJN, et al. Inhibition of the glutaredoxin and thioredoxin systems 
and ribonucleotide reductase by mutant p53-targeting compound APR-246. Sci Rep. 
2018;8(1):12671. doi:10.1038/s41598-018-31048-7 
29.  
Luo J, Solimini NL, Elledge SJ. Principles of Cancer Therapy: Oncogene and Non-
oncogene Addiction. Cell. 2009;136(5):823-837. doi:10.1016/j.cell.2009.02.024 
30.  
Leone G, Teofili L, Voso MT, Lübbert M. DNA methylation and demethylating drugs in 
myelodysplastic syndromes and secondary leukemias. Haematologica. 
2002;87(12):1324-1341. 
31.  
Christman JK. 5-Azacytidine and 5-aza-2′-deoxycytidine as inhibitors of DNA 
methylation: Mechanistic studies and their implications for cancer therapy. 
Oncogene. 2002;21(35 REV. ISS. 3):5483-5495. doi:10.1038/sj.onc.1205699 
32.  
Silverman LR, Demakos EP, Peterson BL, et al. Randomized controlled trial of 
azacitidine in patients with the myelodysplastic syndrome: A study of the cancer and 
leukemia group B. J Clin Oncol. 2002;20(10):2429-2440. doi:10.1200/JCO.2002.04.117 
33.  
Silverman LR, McKenzie DR, Peterson BL, et al. Further analysis of trials with 
azacitidine in patients with myelodysplastic syndrome: Studies 8421, 8921, and 9221 
by the Cancer and Leukemia Group B. J Clin Oncol. 2006;24(24):3895-3903. 
doi:10.1200/JCO.2005.05.4346 
34.  
Fenaux P, Gattermann N, Seymour JF, et al. Prolonged survival with improved 
tolerability in higher-risk myelodysplastic syndromes: Azacitidine compared with low 
dose ara-C: Research paper. Br J Haematol. 2010;149(2):244-249. doi:10.1111/j.1365-

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2141.2010.08082.x 
35.  
VIDAZA (azacitidine for injection), Highlights of Prescribing Information. 2018. 
36.  
Azacitidine. Highlights of Prescribing Information.; 2020. www.fda.gov/medwatch. 
Accessed September 23, 2020. 
37.  
Lee SH, Erber WN, Porwit A, Tomonaga M, Peterson LC. ICSH guidelines for the 
standardization of bone marrow specimens and reports. Int J Lab Hematol. 
2008;30(5):349-364. doi:10.1111/j.1751-553X.2008.01100.x 
38.  
Cheson BD, Greenberg PL, Bennett JM, et al. Clinical application and proposal for 
modification of the International Working Group (IWG) response criteria in 
myelodysplasia. Blood. 2006;108(2):419-425. doi:10.1182/blood-2005-10-4149 
39.  
Cheson BD, Greenberg PL, Bennett JM, et al. Clinical application and proposal for 
modification of the International Working Group (IWG) response criteria in 
myelodysplasia. Blood. 2006;108(2):419-425. doi:10.1182/blood-2005-10-4149 
40.  
Arber DA, Orazi A, Hasserjian R, et al. The 2016 revision to the World Health 
Organization classification of myeloid neoplasms and acute leukemia. Blood. 
2016;127(20):2391-2405. doi:10.1182/blood-2016-03-643544 
41.  
Leroy B, Ballinger ML, Baran-Marszak F, et al. Recommended guidelines for 
validation, quality control, and reporting of TP53 variants in clinical practice. Cancer 
Res. 2017;77(6):1250-1260. doi:10.1158/0008-5472.CAN-16-2179 
42.  
Malcikova J, Tausch E, Rossi D, et al. ERIC recommendations for TP53 mutation 
analysis in chronic lymphocytic leukemia - Update on methodological approaches 
and results interpretation. Leukemia. 2018;32(5):1070-1080. doi:10.1038/s41375-017-
0007-7 
43.  
Leroy B, Fournier JL, Ishioka C, et al. The TP53 website: an integrative resource centre 
for the TP53 mutation database and TP53 mutant analysis. Nucleic Acids Res. 
2013;41(Database issue):D962-9. doi:10.1093/nar/gks1033 
 

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APPENDIX I - Cockcroft-Gault Equation 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Males: 
 
 
Creatinine CL 
(mL/min) 
= 
Weight (kg) × (140 – Age) 
72 × serum creatinine (mg/dL) 
Females: 
 
 
Creatinine CL 
(mL/min) 
= 
Weight (kg) × (140 – Age)  
× 0.85 
72 × serum creatinine (mg/dL) 

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APPENDIX II - ECOG Performance Status 
 
 
 
       Grade 
 
 
0 
 
Fully active, able to carry on all pre-disease performance without 
restriction. 
 
 
1 
 
Restricted in physically strenuous activity but ambulatory and 
able to carry out work of a light or sedentary nature, e.g., light 
housework, office work. 
 
 
2 
 
Ambulatory and capable of all self-care but unable to carry out 
any work activities. Up and about more than 50% of waking hours. 
 
 
3 
 
Capable of only limited self-care, confined to bed or chair more 
than 50% of waking hours. 
 
 
4 
 
Completely disabled. Cannot carry on any self-care. Totally 
confined to bed or chair. 
 
 
5 
 
Dead. 
 
 

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APPENDIX III - Acceptable Contraceptive Methods 
● 
Male or female condom with or without spermicide 
● 
Cervical cap, diaphragm or sponge with spermicide 
Effective Contraceptive Methods That Are User Dependent a  
Failure rate of <1% per year when used consistently and correctly. 
● 
Combined (estrogen- and progesterone-containing) hormonal contraception b 
○ 
Oral  
○ 
Intravaginal  
○ 
Transdermal  
○ 
Injectable 
● 
Progestogen-only hormonal contraception b 
○ 
Oral  
○ 
Injectable  
Effective Methods That Have Low User Dependency  
Failure rate of <1% per year when used consistently and correctly. 
● 
Progesterone-only contraceptive implant b, c  
● 
Intrauterine hormone-releasing system (IUS) b  
● 
Intrauterine device (IUD) 
● 
Bilateral tubal occlusion 
● 
Vasectomized partner  
A vasectomized partner is an effective contraception method provided that the partner is the sole 
male sexual partner of the female of childbearing potential and the absence of sperm has been 
confirmed. If not, an additional effective method of contraception should be used.  
● 
Sexual abstinence  
Sexual abstinence is considered an effective method only if defined as refraining from heterosexual 
intercourse during the entire period of risk associated with the study treatment. The reliability of 
sexual abstinence needs to be evaluated in relation to the duration of the study and the preferred 
and usual lifestyle of the participant.)  
Notes:  
Use should be consistent with local regulations regarding the use of contraceptive methods for 
participants of clinical studies. 
a) Typical use failure rates are lower than perfect-use failure rates (i.e., when used consistently and 
correctly).  
b) If hormonal contraception efficacy is potentially decreased due to interaction with study 
treatment, condoms must be used in addition to the hormonal contraception during the treatment 
period and for at least 120 days, (corresponding to time needed to eliminate study treatment plus 
30 days for study treatments with genotoxic potential) after the last dose of the study treatment. 
c) If locally required, in accordance with Clinical Trial Facilitation Group (CTFG) guidelines, acceptable 
hormonal contraceptives are limited to those which inhibit ovulation.  
 
 
 

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APPENDIX IV - New York Heart Association (NYHA) Classification 
 
NYHA Grading 
MET* 
Class I 
No limitations. Ordinary physical activity does not 
cause 
undue 
fatigue, 
dyspnea 
or 
palpitations 
(asymptomatic LV dysfunction) 
>7 
Class II 
Slight limitation of physical activity. Ordinary physical 
activity results in fatigue, palpitation, dyspnea or 
angina pectoris (mild Congestive Heart Failure (CHF)). 
5 
Class III 
Marked limitation of physical activity. Less than 
ordinary 
physical 
activity 
leads 
to 
symptoms 
(moderate CHF) 
2 – 3 
Class IV 
Unable to carry on any physical activity without 
discomfort. Symptoms of CHF present at rest (severe 
CHF). 
1.6 
 
*MET (metabolic equivalent) is defined as the resting VO2 for a 40-year-old 70-kg man.  
1 MET = 3.5 mL O2/min/kg body weight. 
 
 

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APPENDIX V - Response Criteria for Subjects with MDS and CMML According to 
IWG 2006 Criteria39 
Altering Disease Natural History 
CR 
Bone marrow:  ≤5% myeloblasts with normal maturation of all cell 
lines 
Persistent dysplasia will be noted 
Peripheral blood: 
Hemoglobin ≥11 g/dL 
Platelets ≥100 × 109/L 
Neutrophils ≥1.0 × 109/L 
Blasts 0% 
PR 
All CR criteria if abnormal before treatment, except: 
Bone marrow blasts decreased by ≥50% over pretreatment but still 
>5% 
Cellularity and morphology not relevant 
Marrow CR 
Bone marrow: ≤5% myeloblasts and decrease by ≥50% over 
pretreatment 
Peripheral blood: if HI responses, they will be noted in addition to 
marrow CR 
Stable disease (SD) 
Failure to achieve at least PR, but no evidence of progression for 
>8 weeks 
Failure 
Death during treatment 
Disease progression characterized by worsening of cytopenia, 
increase in % of bone marrow blasts, or progression to a more 
advanced MDS FAB subtype than pretreatment 
Disease Progression (PD) 
For subjects with: 
Less than 5% blasts: ≥50% increase in blasts to >5% blasts 
5-10% blasts: ≥50% increase in blasts to >10% blasts 
10-20% blasts: ≥50% increase in blasts to >20% blasts 
20-30% blasts: ≥50% increase in blasts to >30% blasts 
Any of the following: 
At least 50% decrement from maximum remission/response levels 
in granulocytes or platelets 
Reduction in hemoglobin (Hgb) concentration by ≥ 2 g/dL  
- Transfusion dependence 
Cytogenetic Response 
Complete 
Disappearance 
of 
the 
chromosomal 
abnormality 
without 
appearance of new ones 
Partial 
At least 50% reduction of the chromosomal abnormality 
HI 
Erythroid response (HI-E) 
(Pretreatment <11 g/dL)  
Hgb increase by ≥1.5 g/dL 
Relevant reduction of units of RBC transfusions by an absolute 
number of at least 4 RBC transfusions/8 weeks compared with the 
pretreatment transfusion number in the previous 8 weeks.  Only 

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RBC transfusions given for a Hgb of ≤9.0 g/dL pretreatment will 
count in the RBC transfusion evaluation 
Platelet response (HI-P) 
(Pretreatment <100 × 109/L) 
Absolute increase of ≥30 × 109/L for subjects starting with >20 × 
109/L 
Increase from <20 × 109/L to >20 × 109/L and by at least 100% 
Neutrophil response (HI-N) 
(Pretreatment <1.0 × 109/L) 
At least 100% increase and an absolute increase of >0.5 × 109/L 
 
 
 
Progression/Relapse Criteria for Subjects with MDS/CMML  
 
Altering Disease Natural History 
Disease Progression (PD) 
For subjects with: 
Less than 5% blasts:  ≥50% increase in blasts to >5% blasts 
5-10% blasts:  ≥50% increase in blasts to >10% blasts 
10-20% blasts:  ≥50% increase in blasts to >20% blasts 
20-30% blasts:  ≥50% increase in blasts to >30% blasts 
Any of the following: 
At least 50% decrement from maximum remission/response levels in 
granulocytes or platelets 
Reduction in hemoglobin (Hgb) concentration by ≥2 g/dL  
Transfusion dependence 
Disease transformation 
Transformation to AML (30% or more blasts) 
Relapse after CR or PR 
At least one of the following: 
Return to pretreatment bone marrow blast % 
Decrement of ≥50% from maximum remission/response levels in 
granulocytes or platelets 
- Reduction in Hgb concentration by ≥1.5 g/dL or transfusion 
dependence 
HI 
Progression/relapse after 
HI  
At least one of the following: 
At least 50% decrement from maximum response levels in 
granulocytes or platelets  
Reduction in Hgb by ≥1.5 g/dL 
Transfusion dependence 
 
 
 

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APPENDIX VI - 2016 WHO Classification for CMML and MDS40 WHO CMML 
 
#Not meeting WHO criteria for BCR-ABL1 CML, PMF, PV, or ET. No evidence of PDGFRA, PDGFRB, or FGFR1 rearrangement 
or PCM1-JAK2 (should be specifically excluded in cases with eosinophilia). If myelodysplasia is absent or minimal, 
CMML diagnosis can be made with acquired clonal cytogenetic/molecular genetic abnormality or monocytosis × 3 
months when all other causes of monocytosis have been excluded. Blasts and blast equivalents include myeloblasts, 
monoblasts, and promonocytes 
 
 
WHO Subtype 
Peripheral Blood 
Bone Marrow 
#Chronic Myelomonocytic Leukemia 
*CMML-0 
**CMML-1 
                              ***CMML-2 
 
*<2% blasts 
**≥2% and <5% blasts 
***≥5% and <20% blasts 
persistent monocytosis >1 × 109/L 
   and >10% of differential 
± cytopenias 
Leukocytosis frequent  
*<5% blasts 
**≥5% and 
<10% blasts 
***<20% blasts 
>10% dysplasia 
in affected 
lineage 
***Auer Rods 
The absence of 
the 
Philadelphia 
chromosome 
of bcr-abl 
fusion gene. 
 

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WHO MDS 
 
 
Cytopenias defined as: hemoglobin <10 g/dL; platelet count <100 × 109/L; and absolute neutrophil count <1.8 × 109/L.  
To be classified as dysplasia, >10% of any cell lineage must be dysplastic. PB monocytes must be <1 × 109/L.  
†If SF3B1 mutation is present.  
* Subclassified as MDS-RS with single or multi-lineage dysplasia (MDS-RS-SLD or MDS-RS-MLD). Pancytopenia with RS is 
classified as MDS-RS-MLD.    
** Presence of Auer rods is classified as MDS-EB-2.  
*** Del(5q) alone or with 1 additional abnormality except -7 or del(7q).  
**** 1% peripheral blasts need to be confirmed on 2 separate occasions to make a diagnosis of MDS-U. MDS-U diagnosis is also 
made with SLD and pancytopenia or MDS defining cytogenetic abnormality in the absence of cytopenias.  
 
 
WHO Category 
Peripheral blood 
Bone marrow 
MDS with single lineage dysplasia 
(MDS-SLD) 
Cytopenia (1-2 lines) 
<1% blasts 
 
Dysplasia (1 line) 
<5% blasts 
RS <15%/<5%† 
MDS with ring sideroblasts 
(MDS-RS)* 
Cytopenia (1-3 lines) 
<1% blasts  
 
Dysplasia (1-3 lines) 
 <5% blasts 
RS >15%/>5%† 
MDS with multi-lineage dysplasia 
(MDS-MLD) 
Cytopenia (1-3 lines) 
<1%blasts 
 
Dysplasia (2-3 lines) 
<5% blasts  
RS <15%/<5%† 
MDS with excess blasts type I & II  
(MDS-EB-1 & MDS-EB-2**)  
Cytopenia (0-3 lines) 
Type I: 2-4% blasts 
Type II: 5-19% blasts  
Dysplasia (1-3 lines) 
Type I 5-9% blasts 
Type II 10-19% blasts 
MDS with isolated del(5q)*** 
Cytopenia (1-2 lines) 
<1% blasts 
Dysplasia (1-3 lines) 
< 5% blasts 
MDS unclassified 
(MDS-U)**** 
Cytopenia (0-3 lines) 
1% or <1% blasts 
Dysplasia (1-3 lines) 
<5% blasts 

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APPENDIX VII – TP53 Sequence Variant Interpretation Algorithm 
Inclusion of subjects in the study is based on TP53 sequencing performed in a laboratory at 
each participating site according to established local routines. A study-specific variant 
interpretation algorithm will be used to discriminate between eligible and non-eligible TP53 
sequence variants.  
 
In order to select subjects with high unmet medical need due to poor prognosis, the study 
will enroll subjects that have any TP53 mutation which is not pre-defined as 'benign' or 'likely 
benign'. The operational definition of 'eligible TP53 mutation' in this clinical study therefore 
includes variants classified as pathogenic, likely pathogenic and variant of uncertain 
significance (VUS) in a specified database (UMD-TP53). Subjects harboring at least one such 
TP53 sequence variant are eligible for inclusion, while subjects who only have variant(s) 
classified as benign or likely benign are not eligible. Thus, also TP53 VUS are eligible, avoiding 
exclusion of subjects with possible pathogenic TP53 variants presently classified as VUS. 
 
The basic parameters for TP53 sequencing are listed in Table 17. 
Table 17. Basic parameters for TP53 sequencing and interpretation. 
Sequencing 
method41,42 
• 
Any NGS method (amplicon, hybrid capture) that has 
been validated locally for sequencing TP53 
• 
Covers TP53 exons 2-11 
Data processing41,42 
  
Use HVGS nomenclature: http://varnomen.hgvs.org 
Reference sequences 
• 
genomic:  hg19 or HG38 (do not use hg18) 
• 
cDNA: NM_000546.5 
• 
Protein: NP_000537.3 
Data 
interpretation42,43 
 
5-tier classification of 
functional impact on 
p53: 
Pathogenic, likely 
pathogenic, VUS, 
likely benign, benign 
Pathogenic, likely pathogenic or variant of uncertain 
significance (VUS):  
 
• 
Frameshift mutations 
• 
Nonsense mutations 
• 
Donor / acceptor splice sites +/- 2  
• 
Synonymous mutations with splice impact 
• 
Missense with functional impact 
 
→ Eligible for inclusion in the clinical study 
 
Benign or likely benign: 

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• 
Synonymous mutations without functional impact 
• 
Missense without functional impact* 
 
→ Not eligible for inclusion in the clinical study 
 
*A list derived from the UMD-TP53 database43 is provided as 
common reference for variant interpretation, see Table 18 
and Table 19. 
 
The TP53 sequence variant interpretation algorithm is shown below. 
Figure 4. Algorithm for TP53 variant interpretation. 
 
Abbreviations for pathogenicity criteria: Fr, Ns, Sp, Ps, Ms (Bg = benign). VUS = Variant of 
unknown significance. 
 
Thus, the following criteria (for variant classification or variant type) define each variant 
according to the type of event: 

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Fr - Frameshift, whether they are in or out of frame  
Ns - Nonsense 
Sp - Splice 
Ps - Pathogenic synonymous (according to the list in Table 18) 
Ms - Missense (not in the list of benign variants in Table 19) 
Bg - Benign (relevant to report if multiple variants present in the same subject) 

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The pre-defined lists are presented below, for pathogenic synonymous, Ps (Table 18) and 
benign missense, Bg (Table 19). 
 
Table 18. Listing of synonymous variants with pathogenic splice impact 
cDNA_Variant_ 
NM_000546.5 
NG_017013.2_Variant 
HG19_Variant 
HG38_Variant 
TP53_alpha_ 
NP_000537.3 
c.375G>A 
NG_017013.2:g.16557
G>A 
chr17:g.757931
2G>A 
chr17:g.7675994G>A 
p.T125= 
c.375G>T 
NG_017013.2:g.16557
G>T 
chr17:g.757931
2G>T 
chr17:g.7675994G>T 
p.T125= 
c.375G>C 
NG_017013.2:g.16557
G>C 
chr17:g.757931
2G>C 
chr17:g.7675994G>C 
p.T125= 
c.672G>A 
NG_017013.2:g.17692
G>A 
chr17:g.757817
7G>A 
chr17:g.7674859G>A 
p.E224= 
c.993G>A 
NG_017013.2:g.19016
G>A 
chr17:g.757685
3G>A 
chr17:g.7673535G>A 
p.Q331= 
 
Table 19. Listing of benign or likely benign TP53 variants to be used for exclusion 
cDNA_Variant_ 
NM_000546.5 
NG_017013.2_Variant 
HG19_Variant 
HG38_Variant 
TP53_alpha_ 
NP_000537.3 
c.31G>C 
NG_017013.2:g.15987G>C 
chr17:g.7579882G>C 
chr17:g.7676564G>C 
p.E11Q 
c.91G>A 
NG_017013.2:g.16164G>A 
chr17:g.7579705G>A 
chr17:g.7676387G>A 
p.V31I 
c.139C>T 
NG_017013.2:g.16321C>T 
chr17:g.7579548C>T 
chr17:g.7676230C>T 
p.P47S 
c.145G>C 
NG_017013.2:g.16327G>C 
chr17:g.7579542G>C 
chr17:g.7676224G>C 
p.D49H 
c.173C>G 
NG_017013.2:g.16355C>G 
chr17:g.7579514C>G 
chr17:g.7676196C>G 
p.P58R 
c.215C>G 
NG_017013.2:g.16397C>G 
chr17:g.7579472C>G 
chr17:g.7676154C>G 
p.P72R 
c.217G>A 
NG_017013.2:g.16399G>A 
chr17:g.7579470G>A 
chr17:g.7676152G>A 
p.V73M 
c.248C>T 
NG_017013.2:g.16430C>T 
chr17:g.7579439C>T 
chr17:g.7676121C>T 
p.A83V 
c.319T>C 
NG_017013.2:g.16501T>C 
chr17:g.7579368T>C 
chr17:g.7676050T>C 
p.Y107H 
c.329G>A 
NG_017013.2:g.16511G>A 
chr17:g.7579358G>A 
chr17:g.7676040G>A 
p.R110H 
c.460G>A 
NG_017013.2:g.17399G>A 
chr17:g.7578470G>A 
chr17:g.7675152G>A 
p.G154S 
c.566C>T 
NG_017013.2:g.17586C>T 
chr17:g.7578283C>T 
chr17:g.7674965C>T 
p.A189V 
c.665C>T 
NG_017013.2:g.17685C>T 
chr17:g.7578184C>T 
chr17:g.7674866C>T 
p.P222L 
c.704A>G 
NG_017013.2:g.18292A>G 
chr17:g.7577577A>G 
chr17:g.7674259A>G 
p.N235S 
c.847C>T 
NG_017013.2:g.18778C>T 
chr17:g.7577091C>T 
chr17:g.7673773C>T 
p.R283C 
c.869G>A 
NG_017013.2:g.18800G>A 
chr17:g.7577069G>A 
chr17:g.7673751G>A 
p.R290H 
c.883C>T 
NG_017013.2:g.18814C>T 
chr17:g.7577055C>T 
chr17:g.7673737C>T 
p.P295S 
c.935C>G 
NG_017013.2:g.18958C>G 
chr17:g.7576911C>G 
chr17:g.7673593C>G 
p.T312S 
c.1015G>A 
NG_017013.2:g.21857G>A 
chr17:g.7574012G>A 
chr17:g.7670694G>A 
p.E339K 

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c.1073A>T 
NG_017013.2:g.21915A>T 
chr17:g.7573954A>T 
chr17:g.7670636A>T 
p.E358V 
c.1079G>C 
NG_017013.2:g.21921G>C 
chr17:g.7573948G>C 
chr17:g.7670630G>C 
p.G360A 
c.1096T>G 
NG_017013.2:g.21938T>G 
chr17:g.7573931T>G 
chr17:g.7670613T>G 
p.S366A 
 

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 Examples of results: 
 
HG19_Variant 
cDNA_Variant 
_NM_000546.5 
TP53_alpha_NP_000537
.3 
Criterion 
chr17:g.7578406G>A 
c.524G>A 
p.R175H 
Ms 
Missense variant hot spot 
 
HG19_Variant 
cDNA_Variant 
_NM_000546.5 
TP53_alpha_NP_000537
.3 
Criterion 
chr17:g.7578212C>T 
c.637C>T 
p.R213* 
Ns 
Nonsense variant hot spot 
 
HG19_Variant 
cDNA_Variant 
_NM_000546.5 
TP53_alpha_NP_000537
.3 
Criterion 
chr17:g.7578223_7578222
del 
c.626_627del 
p.(R209Kfs*6) 
Fr 
Indel variant hot spot (deletion) 
 
HG19_Variant 
cDNA_Variant 
_NM_000546.5 
TP53_alpha_NP_000537
.3 
Criterion 
chr17:g.7579471dup 
c.216dup 
p.(V73Rfs*76) 
Fr 
Indel variant hot spot (duplication) 
 
HG19_Variant 
cDNA_Variant 
_NM_000546.5 
TP53_alpha_NP_000537
.3 
Criterion 
chr17:g.7574005_7574004ins
A 
c.1022_1023ins
A 
p.(F341Lfs*6) 
Fr 
Indel variant hot spot (Insertion) 
 
HG19_Variant 
cDNA_Variant 
_NM_000546.5 
TP53_alpha_NP_000537
.3 
Criterion 
chr17:g.7578555G>A 
c.376-1G>A 
p.? 
Sp 
Splice site variant 
 
HG19_Variant 
cDNA_Variant 
_NM_000546.5 
TP53_alpha_NP_000537
.3 
Criterion 
chr17:g.7579312G>A 
c.375G>A 
p.T125= 
Ps 
Pathogenic synonymous variant  
 
HG19_Variant 
cDNA_Variant 
_NM_000546.5 
TP53_alpha_NP_000537
.3 
Criterion 

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chr17:g.7579472C>G 
c.215C>G 
p.P72R 
Bg 
chr17:g.7578210A>G 
c.639A>G 
p.R213= 
Bg 
Non-pathogenic common SNPs 
 
HG19_Variant 
cDNA_Variant 
_NM_000546.5 
TP53_alpha_NP_000537
.3 
Criterion 
chr17:g.7578561C>T 
c.376-7C>T 
p.(=) 
Bg 
Intronic mutation