Targeting Non-Genetic Mechanisms to Overcome Therapy Resistance in Myeloid Leukemia Restricted; Files Only

Abstract

Resistance to therapy remains a major barrier to cure in acute leukemia, underscoring the need for functional approaches that can predict therapeutic response beyond genomic information alone. This part of the work employs mitochondrial apoptotic profiling and single-cell multiomics strategies to uncover survival dependencies and adaptive resistance programs in both T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML).

In the first part, we define the anti-apoptotic landscape of adult T-ALL using functional BH3 profiling, revealing that early T-cell precursor (ETP) and non-ETP subtypes both show predominant dependence on BCL-2, with subsets displaying mixed BCL-2/BCL-XL co-dependence. These dependencies translated into robust ex vivo sensitivity to venetoclax, and the identification of HRK enrichment suggested a BCL-XL contribution in a subset, supporting combined BH3-mimetic strategies (venetoclax + navitoclax) as a rational therapeutic approach for adult T-ALL.

The second part focused on extending this functional approach to AML by developing patient-derived xenograft (PDX) models to map mitochondrial priming in drug-naïve and resistant models and to identify mechanisms of multidrug resistance. Dynamic BH3 profiling (DBP) effectively distinguished treatment-naïve and pretreated samples, accurately predicting in vivo responses across diverse mechanisms of action. Acquisition of multidrug resistance was consistently accompanied by diminished mitochondrial priming, providing a unifying mechanism of resistance that remained functionally measurable even when genomic markers were silent. These results established a reduction in apoptotic priming as a non-genetic mechanism of resistance in AML.

Finally, to understand the minimal residual state in leukemia and to dissect the origins and plasticity of drug-tolerant states, we combined single-cell lineage tracing with multimodal profiling (snRNA-seq + snATAC-seq) to characterize persister populations in AML during cytotoxic and targeted therapies. We observed reversible persistence, altered apoptotic priming, and non-genetic clonal adaptation within single parental lineages, highlighting a dynamic, transient reservoir that fuels relapse.

Together, these studies delineate the apoptotic landscape and adaptive survivorship programs in acute leukemia, demonstrating that functional profiling of mitochondrial priming can predict therapeutic response and reveal vulnerabilities that can be exploited through rational drug combinations. This work advances a framework for integrating functional and single-cell analyses into precision leukemia therapy to overcome both intrinsic and acquired drug resistance.

Table of Contents

Abstract v

Acknowledgements vi

Table of contents vii

List of Figures x

List of Supplementary Figures xi

List of Tables xii

List of Supplementary Tables xii

List of Abbreviations xii

Chapter 1 : INTRODUCTION 1

A. T-cell Acute lymphoblastic leukemia (T-ALL) 2

B. Acute myeloid leukemia (AML) 4

C.  Apoptotic priming, dependence and BCL-2 family 8

D.  Drug resistance mechanisms in AML 12

E.  Statement of Problem 19

Chapter 2 : BH3 PROFILING IDENTIFIES BCL-2 DEPENDENCE OF ADULT EARLY T-CELL PROGENITOR ACUTE LYMPHOBLASTIC LEUKEMIA PATIENTS 23

A.  Abstract 25

B.  Introduction 26

C.  Experimental Procedures 27

D.  Results 30

E.  Discussion 36

F.  Acknowledgements 38

G.  Contribution 38

H.  Supplementary materials 44

Chapter 3 : ACQUIRED MULTIDRUG RESISTANCE IN AML IS CAUSED BY LOW APOPTOTIC PRIMING IN RELAPSED MYELOBLASTS 48

A.  Abstract 50

B.  Introduction 51

C.  Experimental procedures 54

D.  Results 61

E.  Discussion 78

F.  Acknowledgements 82

G.  Contribution 83

H.  Supplementary materials 98

Chapter 4 : SINGLE CELL LINEAGE TRACING REVEALS UNIQUE EVOLUTIONARY PATHS TO PERSISTERS IN ACUTE MYELOID LEUKEMIA 116

A.  Abstract 117

B.  Introduction 118

C. Methods 119

D. Results 130

E. Discussion 145

F. Contribution 147

G. Supplementary material 162

Chapter 5 : DISCUSSION 171

A. Implications of T-ALL apoptotic dependence study 171

B. Implications from apoptotic priming studies in AML PDXs 174

C. Implications from AML persisters study 180

Chapter 6 :  REFERENCES 187

About this Dissertation

Rights statement

• Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.

School	Laney Graduate School
Department	Biological and Biomedical Sciences
Subfield / Discipline	Cancer Biology
Degree	Ph.D.
Submission	Dissertation
Language	English
Research Field	Biology, Genetics Biology, Cell Health Sciences, Oncology
Keyword	Drug tolerant Persisters Non-genetic resistance Single cell multiomics Lineage tracing BH3 mimetics Acute myeloid leukemia
Committee Chair / Thesis Advisor	Bhatt, Shrutiben, Emory University
Committee Members	Frank, David, Emory University Shanmugam, Malathy, Emory University Boise, Lawrence, Emory University Moffitt, Andrea, Emory University Lesinski, Gregory, Emory University

Last modified

Primary PDF

Thumbnail	Title	Date Uploaded	Actions
	File download under embargo until 27 May 2028	2026-04-16 10:50:12 -0400	File download under embargo until 27 May 2028

Supplemental Files

Thumbnail	Title	Date Uploaded	Actions