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Book-Nutrigenomics 1stpreview
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Nutrigenomics
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Nutrigenomics
Nutrigenomics
Carsten Carlberg • Stine Marie Ulven
Ferdinand Molnár
Nutrigenomics
Carsten Carlberg Stine Marie Ulven
Institute of Biomedicine Department of Nutrition
University of Eastern Finland University of Oslo
Kuopio, Finland Oslo, Norway
Ferdinand Molnár
School of Pharmacy
University of Easterm Finland
Kuopio, Finland
Our daily diet is more than a collection of carbohydrates, lipids and proteins that
provide energy and serve as building blocks of our life; our diet is also the most
dominant environmental signal to which we are exposed from womb to death. The
fascinating area of nutrigenomics analyses this daily communication between diet,
food and nutrients, their metabolites and our genome. This book describes how
nutrition shapes human evolution and demonstrates its consequences for our sus-
ceptibility to diseases, such as diabetes and atherosclerosis. Inappropriate diet can
yield stress for our cells, tissues and organs and then it is often associated with low-
grade chronic inflammation. Overnutrition paired with physical inactivity leads to
overweight and obesity and results in increased burden for a body that originally
was adapted for a life in the savannas of East Africa. Therefore, this textbook does
not discuss a theoretical topic in science, but it talks about real life and our life-long
“chat” with diet. We are all food consumers, thus each of us is concerned by the
topic of this book and should be aware of its mechanisms.
The availability of the sequence of the complete human genome and the conse-
quent development of next-generation sequencing technologies have significantly
affected nearly all areas of bioscience. This new knowledge was the starting point
for new disciplines, such as genomics and its sub-discipline nutrigenomics. The lat-
ter comprises not only the variation of the human genome, such as single nucleotide
polymorphisms (SNPs), but also the dynamic packaging of the genome into chro-
matin including all information stored in this epigenome. Moreover, this book
describes the proteins that are involved in the signal transduction between dietary
molecules and the genome, such as nuclear receptors, chromatin modifiers and
energy status-sensing kinases, and their mechanism of action.
The purpose of this book is to provide an overview on the principles of nutrige-
nomics and their relation to health or disease. We are not aiming to compete with
more comprehensive textbooks on molecular nutrition, evolutionary biology, geno-
mics, gene regulation or metabolic diseases, but rather will focus on the essentials
and will combine, in a compact form, elements from different disciplines. In order
to facilitate the latter, we favour a high figure-to-text ratio following the rule “a pic-
ture tells more than thousand words”.
v
vi Preface
The content of this book is based on the lecture course “Nutrigenomics”, which
is held since 2003 once per year by one of us (C. Carlberg) at the University of
Eastern Finland in Kuopio. The book is subdivided into 3 sections and 12 chapters.
Following the “Introduction”, there are sections on the “Molecular genetic basis”
and the “Links to disease”, which take a view on nutrigenomics from the perspec-
tive of molecular mechanisms or from the causes of metabolic diseases,
respectively.
This book is primarily designed for master level students of biosciences, but may
also be used by students of other biomedical disciplines and by PhD students. The
book has five major learning objectives. Students should:
(i) Get an overview on human variation on the level of the genome and epigenome,
in response to dietary molecules and the regulatory proteins involved in the
respective signal transduction processes
(ii) Have an understanding of the diseases that are strongly associated with dietary
intake and physical inactivity, such as obesity, type 2 diabetes, atherosclerosis
and the metabolic syndrome
(iii) Recognize the key components and mechanisms in nutrigenomics and the mul-
tiple layers of its regulatory complexity
(iv) Show the ability to analyze the human genome and epigenome and its variation
in nutrition sensing and information processing processes, i.e. to judge their
impact for on the complex etiology of metabolic diseases
(v) Apply knowledge in nutrigenomics in designing, performing and analyzing
respective experiments, such as quantitative PCR, RNA-seq or ChIP-seq
We hope the readers will enjoy this demonstrative book and get as enthusiastic
about the topic of nutrigenomics as the authors do.
The authors would like to thank Reinhard Bornemann, MD, PhD, Marjukka
Kolehmainen, PhD, Vibeke Telle-Hansen, PhD, and Jenni Puurunen, MSc, for
extensive proofreading and constructive criticism.
vii
Contents
Part I Introduction
1 Nutrition and Common Diseases ........................................................... 3
1.1 Human Nutrition ............................................................................ 3
1.2 Nutrition and Obesity ..................................................................... 8
1.3 Nutrition and Cancer ...................................................................... 9
1.4 Nutrition and Diabetes ................................................................... 11
1.5 Nutrition and Cardiovascular Diseases .......................................... 13
1.6 Impact of Exercise.......................................................................... 20
Additional Reading ................................................................................... 23
2 Human Genomic Variation .................................................................... 25
2.1 Migration and Evolutionary Challenges of the Modern
Human ............................................................................................ 26
2.2 Diversity of Human Populations .................................................... 27
2.3 Genetic Variants of the Human Genome ........................................ 30
2.4 The HapMap Project and Haplotype Blocks ................................. 33
2.5 Genome-wide Association Studies................................................. 35
2.6 Whole Genome Sequencing and the 1000 Genomes
Project ............................................................................................ 40
Additional Reading ................................................................................... 44
ix
x Contents
1,25(OH)2D3 1,25-dihydroxyvitamin D3
25(OH)D3 25-hydroxyvitamin D3
5,10-MTHF 5,10-methylene THF
α-MSH α-melanocyte-stimulating hormone
ABC ATP-binding cassette
ABL abetalipoproteinemia
AC adenylate cyclase
ACAT1 acetyl-CoA acetyltransferase 1
ACC acetyl-CoA carboxylase
ACL ATP citrate lyase
ADRB3 adrenoceptor beta 3
AGRP agouti-related peptide
AKT Akt murine thymoma viral oncogene homolog
ALA α-linolenic acid
ALOX5 arachidonate 5-lipoxygenase
ALOX15 arachidonate 15-lipoxygenase
AMPK adenosine monophosphate-activated protein kinase
AMY1 amylase
ANGPTL2 angiopoietin-like protein 2
APEH N-acylaminoacyl-peptide hydrolase
AP-1 activating protein 1
APO apolipoprotein
AR androgen receptor
ARL4C ADP-ribosylation factor-like
ARNTL aryl hydrocarbon receptor nuclear translocator-like
ASC apoptosis-associated speck
ASIP agouti signaling protein
ATF6 activating transcription factor 6
ATM ataxia telangiectasia mutated
atRA all-trans retinoic acid
β-OHB β-hydroxybutyrate
xiii
xiv Abbreviations