Effective Drug Treatment Induces Drug Resistance Through Rapid Genome Alteration-Mediated ...

153 Pages·2016·11.65 MB·English

Wayne State University
Wayne State University Dissertations
1-1-2016
Effective Drug Treatment Induces Drug Resistance
Through Rapid Genome Alteration-Mediated
Cancer Evolution
Steven Horne
Wayne State University,
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Recommended Citation
Horne, Steven, "Effective Drug Treatment Induces Drug Resistance Through Rapid Genome Alteration-Mediated Cancer Evolution"
(2016).Wayne State University Dissertations.Paper 1543.
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EFFECTIVE DRUG TREATMENT INDUCES DRUG RESISTANCE THROUGH
RAPID GENOME ALTERATION-MEDIATED CANCER EVOLUTION

by
STEVEN DOUGLAS HORNE
DISSERTATION
Submitted to the Graduate School
of Wayne State University,
Detroit, Michigan
in partial fulfillment of the requirements
for the degree of
DOCTOR OF PHILOSOPHY
2016
MAJOR: MOLECULAR BIOLOGY AND
GENETICS

Approved By:

Advisor Date
© COPYRIGHT BY
STEVEN DOUGLAS HORNE
2016
All Rights Reserved
DEDICATION
For Candice, River and Miles
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ACKNOWLEDGMENTS
Many people have helped me get through the ‘stress’ and ‘chaos’ over
these last six years, and they all certainly deserve recognition.
I cannot completely put into words how lucky and grateful I am to have
had Dr. Henry Heng as my advisor. Simply put, Dr. Heng was phenomenal. He
offered me a seemingly endless amount of opportunities and resources to grow
as a thinker, as a student, as a writer, as a presenter, as a mentor, and as a
scientist. In addition to his generosity, he was an advocate for me, and he was
incredibly patient with me as I worked through the growing pains of being a
doctoral student. He saw qualities in me that I did not. He believed in me when I
would not. I credit Dr. Heng for all the success I experienced during my time at
Wayne State; none of this would have been possible without him. Dr. Heng is
truly an ‘outlier’ in academia: brilliantly creative and fearless. I admire him dearly,
and I wish him only the best.
I also had a fantastic dissertation committee, consisting of Dr. Alexander
Gow, Dr. Derek Wildman and Dr. Gen Sheng Wu. I thank them all for spending
their time enriching this project and for the great conversations we had over the
years.
I thank the past and present members of the Heng Lab for their support.
Dr. Joshua Stevens was an absolute pleasure to work with and an excellent
writer and scientist. I thank Guo Liu for his assistance and kindness over the
years. Of course, I could not imagine getting through the program without Dr.
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Batoul Abdallah. My ‘big sister’ in graduate school, she was always there for
guidance, lending an ear to vent into, or for a walk for a cup of coffee. I am
fortunate to have been a part of such a special group.
I extend my thanks and gratitude to the faculty and staff at the CMMG for
their support over the past six years, in particular Dr. Lawrence Grossman,
Suzanne Shaw (who saved me more than a couple of times) and David
Wissbrun. I also want to give a special thanks to Dr. Gregory Kapatos and Dr.
Stephen Krawetz. Dr. Kapatos made me feel welcome at CMMG and was in my
corner from day one. Dr. Krawetz was incredibly generous and offered me a
head start in the program by spending a summer as a research assistant in his
lab. I learned a great deal in that short time; many of the skills I gained there
helped me throughout my studies.
I thank the friends I made at Wayne State for their support and the great
times we shared. There are too many to list, but I will acknowledge the six I
started this journey with: Dr. Roberto Mendez, Dr. Sidra Ahsan, Dr. Nermin
Gerges, Daniel Radecki, Chris Sinkler and Emily Wood, as well as Dr. Paul
Albosta, Dr. Kathleen Maheras, Dr. Graham Johnson, Dr. Aaron Burr, Seema
Shae, Christion Hall, Rick Smith, Dr. Daochun Sun, Dr. Ze Zhang, Dr. Allison
Gartung, April Kusowski, and the students at CMMG. I hope our paths cross
again, preferably during a happy hour.
I am forever grateful for the love and support from my family. I cannot
thank my mom enough for all she has done for me over the years both for me
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and my family. She is a terrific mother and grandmother. I thank my brother Dan
and my (soon-to-be) stepdad Frank for their limitless support, and I thank my
aunt Diane and my uncle Mike for their generosity and the special interest they
have had in my education since I was a child. I have not forgotten about you
Grandma; we are still missing you.
Last, and furthest from least, I thank my beautiful wife Candice and my
incredible boys River and Miles for their love, inspiration, support and patience.
Candice has been an amazing mother and partner in life, and I thank her for the
many sacrifices she made to make this possible. Without any complaint, she
orchestrated the family ‘business’ while I was spending long nights working in the
lab, cramming for exams, or writing manuscript drafts at all-night coffee shops.
She was a source of much-needed rationality for me, and she was always there
to put life’s little curveballs back into perspective. River and Miles, having
accomplished so much already in their little lives, are inspiring. They brightened
the darkest of my days, and I cannot do anything without them in mind. My wife
and kids have been nothing short of wonderful, and they are the three reasons
why I finished this journey.

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TABLE OF CONTENTS
DEDICATION ................................................................................................... ii
ACKNOWLEDGMENTS ................................................................................... iii
LIST OF TABLES ............................................................................................ ix
LIST OF FIGURES ........................................................................................... x
CHAPTER 1: INTRODUCTION ....................................................................... 1
Cancer drug resistance represents a significant challenge in
current cancer therapeutics ................................................................... 1

Current molecular understandings of cancer drug resistance ............... 5
Macro-cellular evolution mediated genome heterogeneity plays
a critical role in cancer drug resistance ............................................... 11

The adaptive function of stress-induced genome alteration ................ 15
The majority of cancer drug resistance research and discussion
has neglected the macro-cellular evolutionary phase of cancer ......... 17

Overview ............................................................................................. 19
CHAPTER 2: EFFECTIVE DRUG TREATMENT INDUCES DRUG
RESISTANCE THROUGH RAPID GENOME ALTERATION-
MEDIATED CANCER EVOLUTION .................................................... 21

Introduction ......................................................................................... 21
Methods and materials ........................................................................ 23
Results ................................................................................................ 26
Discussion ........................................................................................... 40
CHAPTER 3: SEARCHING FOR A CONCEPTUAL FRAMEWORK TO
STUDY THE PATTERN OF CANCER EVOLUTION THAT
ACCOUNTS FOR HETEROGENEITY AND OUTLIER
CONTRIBUTIONS ............................................................................... 49

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Introduction ......................................................................................... 49
Different analytical approaches lead to drastically different
conclusions.......................................................................................... 52

Defining key parameters for studying heterogeneous
populations under stress ..................................................................... 57

Implications for experimental design and data presentation ............... 58

Research focus must be shifted to single cell level resolution ............ 60

Prioritization of genetic levels is necessary for constructing
accurate understandings of complex diseases ................................... 60

Classification of biomedical research studies will aide in
selecting informative analytical approaches ........................................ 61

Why we have trouble confirming results through experiment
replication in cancer research (and beyond) ....................................... 64

CHAPTER 4: CONCLUSIONS AND FUTURE DIRECTIONS ....................... 66

Application of genome theory resulted in the identification of
a general, drug-induced macro-cellular evolutionary mechanism
of cancer drug resistance .................................................................... 66

Establishment of a conceptual framework to study the pattern
of cancer evolution that accounts for heterogeneity and outlier
contributions ........................................................................................ 68

Implications of drug-induced genome-mediated cancer drug
resistance on current large-scale research efforts, treatment
administration and cancer drug development ..................................... 69

Expansion of this project by incorporation of additional models
and treatment strategies will confirm the general role of drug-
induced macro-cellular evolution in cancer drug resistance ............... 74

Identification of a treatment “balancing act” consisting of cancer
genome constraint and tumor cell population control would
provide insight for future treatment regimen development .................. 74

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Extensive profiling of aggressive outliers and genome chaos
will be necessary to further understand the relationship between
different levels of genetic change and emergent features .................. 75

APPENDIX A: HEMACYTOMETER-BASED CELL COUNTING
RESULTS OF SIX DOXORUBICIN HIGH-DOSE TREATMENT
TRIALS ................................................................................................ 77

APPENDIX B: HEMACYTOMETER-BASED CELL COUNTING
RESULTS OF THREE DOXORUBICIN LOW-DOSE
TREATMENT TRIALS ......................................................................... 88

APPENDIX C: SINGLE CELL-DERIVED POPULATION GROWTH
OF UNTREATED AND RECOVERED HCT116 CELLS ..................... 94

APPENDIX D: HORNE SD, STEVENS JB, ET AL. (2013). “WHY
IMATINIB REMAINS AN EXCEPTION OF CANCER
RESEARCH.” J CELL PHYSIOL 228(4): 665-670 .............................. 96

APPENDIX E: HORNE SD, POLLICK SA, ET AL. (2015).
“EVOLUTIONARY MECHANISM UNIFIES THE HALLMARKS OF
CANCER.” INT J CANCER 136(9) 2012-2021 ................................. 102

APPENDIX F: HORNE SD, YE CJ, ET AL. (2015).
“CHROMOSOMAL INSTABILITY (CIN) IN CANCER.” ELS: 1-9 ...... 112

REFERENCES ............................................................................................. 121

ABSTRACT .................................................................................................. 139

AUTOBIOGRAPHICAL STATEMENT ......................................................... 141

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