Epigenetic modification of mitochondrial genes in Alzheimer's disease

342 Pages·2017·6.57 MB·English

Epigenetic modification of mitochondrial genes in Alzheimer’s disease
(AD)

Submitted by
Matthew Adrian Michael Devall
to the University of Exeter
as a thesis for the degree of
Doctor of Philosophy in Medical Studies
in April 2017

This thesis is available for Library use on the understanding that it is copyright
material and that no quotation from the thesis may be published without proper
acknowledgement.

I certify that all material in this thesis which is not my own work has been
identified and that no material has previously been submitted and approved for
the award of a degree by this or any other University.

Signature………………………………………………………….

1
Abstract

Alzheimer’s disease is a chronic, neurodegenerative disease characterised by
amyloid plaque accumulation, neurofibrillary tangles and eventual neuronal cell
loss. The complex aetiology exhibited in late-onset Alzheimer’s disease
presents a considerable challenge in the field of genetics, with identified
variants from genome-wide association studies collectively only explaining
about a third of disease incidence. As such, new avenues are being explored to
elucidate underlying mechanisms associated with disease onset and
progression.

In 2014, the first epigenome-wide association studies in Alzheimer’s disease
were published, identifying several, novel differentially methylated loci in the
nuclear genome in cortical brain samples, highlighting that epigenetic
mechanisms may play a role in disease aetiology. Further, a growing body of
evidence has implicated mitochondrial dysfunction as an early feature of
disease pathogenesis. Despite this, few studies have investigated the role of
mitochondrial DNA epigenetics in Alzheimer’s disease. Indeed, the relatively
nascent field of mitochondrial epigenetics has largely been restricted to
candidate-based gene approaches to identify differential methylation associated
with disease.

The main aim of this thesis was therefore to design an experimental and
bioinformatic pipeline for the analysis of mitochondrial DNA methylation in post-
mortem human brain tissue; first in healthy non-demented control donors, and
2
subsequently in individuals with Alzheimer’s disease. Our work therefore
represents the first epigenome wide studies of mitochondrial DNA methylation
at single nucleotide resolution, providing a framework not only for mitochondrial
DNA methylation in Alzheimer’s disease, but also in a number of complex
diseases characterised by mitochondrial dysfunction.

3
Acknowledgements
“I drink and I know things” Tyrion Lannister.

Never have truer words been spoken!

I’m sure at this time, I should write much more sensible and deeper quotes that
have inspired me through my PhD, quotes that I turn to when times are tough,
but in truth, quotes don’t inspire me. The people that I acknowledge below
however have made my time in Exeter, and now Utrecht, something that I will
never forget!

First and foremost, I would like to thank my parents, my grandfather and
my sisters for their continued love and support. There’s nothing more
inspiring in this world than having a fantastic role model to look up to, and in my
father, I have been blessed. Never have I met a man who has worked so hard
to provide for their family and to care so wholeheartedly about their wellbeing.
My best bud, it looks like we have made it across the finish line! In many ways,
it still feels so recent that I left for Exeter and was left wondering, ‘well now
what?’ But you have always been my centre, even if we don’t always see eye to
eye! I thank my mother for keeping me company on any walk that takes more
than five minutes, if only my phone bill was as loving to me as you have been!
The amount of times you must have wondered over the years if you could make
it through the day without hearing me moan about one ‘crisis’ or another must
be staggering! I thank my sisters Ellen, Charmayne and Ashleigh for always
4
being there when needed, in particular Ashleigh whose regular visits always
makes sure that I was never more than a month or two without an oatcake!
Leaving the country has been especially stressful at times, but your warm words
and care have never been far from my heart.

My warmest thanks go out to the epigenetics group and to my PhD
supervisors, Katie, Jon and Mike. Without their kind support and honest
words, I would not be sitting here, writing this. When given the chance to reflect,
I feel that the drunken stupidity, the annual midweek breakdowns, the lengthy
‘meetings’ in Mike’s office spent discussing the world and the benefits of
internet dating, have given me the strength, or sometimes just the ventilation
needed to continue driving forward. I am very grateful to each of you for the
generosity, understanding and confidence that you have shown me over the
years and I hope I haven’t been too much of a pain!

In addition, a more personal thank you should really be extended to Katie!
I would like to thank you Katie from the bottom of my heart for all of the hard
work you have put in throughout the last three and a half years. Not only has
your support stopped me from falling to pieces on a professional level, but you
have also been there on a personal level on more than one occasion, far
exceeding your duties as a supervisor.

To my best friend Myles, I thank you for all that you have ever done for me,
and for coming up for a question to ask at ‘that induction’. I thank you for not
5
giving up on me when many others would have. When I first arrived, my social
anxiety was quite easily at an all-time high and your continued persistence for
me to join the group for a drink will always remain one of the most important
social events in my life. From that Tuesday evening in Firehouse, I knew that I
had found a friend, a brother, for life. Since then I have had so many good
memories to treasure, whether it be Pizza Sundays in the apartment with
Hannah, dragging you to Timepiece or getting lost in Prague, I have been lucky
to know you. I don’t think that I will ever forget the sheer fear of that Prague
mishap and the embrace I was taken into when I finally found my way back,
scarred by what I had seen! It seems odd to have to summarise a brotherhood
in such a small space and I do not do you justice with this, but I love you my
friend and I look forward to knowing you for so many years to come.

Jenny, my dearest friend and tea lover! I knew you were less quiet than you
pretend to be from the first day that I met you! I am sorry that I am seemingly
very poor with directions to Mosaic, I really had no excuse for that. I have
missed our prosecco and movie nights in recent months. I cannot watch Forrest
Gump now without thinking of you, nor Big Hero 6, nor Emperor’s New….well
you get the idea. With four sisters already, you wouldn’t think that I would find
another, but yet, here you are! In all of my time in Exeter, I have never met a
sweeter, more honest individual who just understands, and yet still, surprisingly
accepts me, and for that, thank you! Perhaps now that I have left, you may
finally get chance to carry on with some work, absent of regular coffee breaks,
over-exuberant hugs and ‘surprising’ dilemmas; because quite frankly, no one
says ‘what did you do now’ with as much frequency and despair as you have to
6
me since you arrived. Thank you for always being there and for your continued
advice and support.

To Jeff, someone who has always had my back! I don’t think I’ve ever met
anyone who jumps into the geopolitical landscape of the world or how the
planet’s current state of affair was brought about by an unbroken chain of
events that was determined by the very first interactions to ever be had. I must
admit, I’m usually a couple in by this time and so I probably missed quite a bit of
what you actually strove for in your continued attempts to convert me to
determinism, but it has always been fun to listen to nonetheless! Looking back
on my time in this city, I really can’t say that I would have come close to
enjoying it without a spontaneous trip to the pub or a round of ‘who loves Marvel
the most’, which I always inevitably win of course! Thank you for helping me get
to this point, now keep away from my sister!

Joe and Nyree, also known as my adopted parents! Thank you for allowing
me to (almost) conquer my unease around snakes, and to opening my eyes to
the pagan culture. I very much hope that I can tag along to Edinburgh in the
near future to see it in all its glory! Of course, I could just go to
Glastonbury….Moving on from those F’s and C’s, thank you for showing me the
true Devon, my final summer here has given me some fantastic experiences, I
even got to spear fish, kind of, (thank god for sausages!). I’m very glad that in
return I introduced you to Cards Against Humanity, and you plundered their
reserves for every card that ever existed! I will miss our irregular coffee and
lunch run (drives) and all of the wisdom that you have imparted upon me over
7
said times. Lord knows it must have been like banging your head against a brick
wall at times! I look forward to seeing you both in Utrecht next year!

Baz, I still think that I’m scared of you! I’m pretty sure the first word you said to
me would have been subtitled as an ‘indiscernible grunt’. But as I stifle past this,
I thank you for being there to help me troubleshoot, for being the only other
person who seemingly like’s football in Devon, (even if that does make you an
Arsenal fan), and for the long discussions on Star Wars, Marvel, DC and
general gaming. Importantly, Barry you will always hold the honour of being the
person to introduce me to the Witcher, and whilst I’ve never cared much for
cards, if Gwent was a real game, I would now be bankrupt! Thanks for
everything!

Janou, it’s quite incredible that the first time you were in Exeter, we rarely
spoke. Thank God this changed the second time. Your warmth and generosity
made my last few months in Exeter truly happy, despite even the terrible
attempt at a German market. Going to tar barrels in Ottery St Mary remains one
of my happiest evenings in my time here, despite the million and one people
that were there. I just hope that no matter how lost we get in the future, we will
just be one ‘cacaw’ away for each other.

Bex, I actually still think I’d be doing the MeDIP paper now if you hadn’t have
arrived when you did! It still makes me laugh when I think about the time you
were so shocked that I called you a nerd, I mean Bex, come on! Thank you for
8
introducing me to board games, even if I must be silent whilst playing them!!
Here was I thinking that all board games involved some exchange of money for
properties around a board, how wrong I was. I have always known where I
stand with you duck, (usually outside of punching distance) and that is
something that I have always appreciated! Also, you make a mean bacon
sandwich.

Marta and Eleni, you have both made my first months in Utrecht very
interesting in your own ways. To move to a new city whilst writing a thesis and
starting a new position left me in a place of fear and doubt. You have both been
there to provide support, to enjoy in the good times, to keep my glass half full
(with beer, or coffee (or both)) and to make me feel so very welcome. For this, I
thank you all.

Abhi, ah Abhi, for without you I would about to become homeless! Is there
anything more to say? Well yes, there is much. I’m very happy to have met you,
to have been forced into the motherlands of nowhere (Cinemec) to watch one of
the worst films of my life (Kong) and to enjoy my first shisha and first ziplining.
WTFN. I really hope that we make sure to do our trip of Europe next year!

Gio, you’ve quickly become like a brother to me in recent months, largely
because we spend about 8 hours (sleeping) apart before you have to endure
my presence further! It has been great to have a gym buddy back, to go out for
random drinks and be introduced to whole new genres of music. It isn’t often
9
that you meet someone with so many different passions and such varied
interests. A conversation with you is never anything other than entertaining. I
wish you all the best of luck in the future for getting your own Ph.D, but more
than that, I look forward to many trips to experience true Italian culture with you!

Carlos: you my friend, are an enigma! You introduced me to nightlife in Utrecht
and Amsterdam, and no matter when (if) I ever read this again, I will probably
still have your jeans! It’s always amazing to meet someone with such a good
heart who truly cares for others. I have really appreciated the last few months,
introducing me to Brian and Miguel and am hoping to one day get my full
initiation to ‘the terror squad’!

Stefania, it’s great to get to meet someone in the last couple of months of your
thesis who is full of kindness and good spirit, who helps to get you away from
the tortures of writing, and whose honesty and wisdom are so strong. In you
Stefania, I met that person and whilst it’s a shame our stays in Exeter didn’t
overlap for too long, you have made a true impression on me and I hope to see
you in Utrecht very soon (and often!).

Lastly Artemis, for everything that you have done for me and for the courage
that you have given me, I will be eternally grateful. No single person has ever
had such a strong, positive impact on my life, that will never be forgotten.

10