Diet and Lifestyle MDL Ebook

Methylation Diet and Lifestyle
Dr. Fitzgerald received her doctorate of naturopathic medicine from National College of Natural
Medicine in Portland, Oregon. She completed the first CNME-accredited post-doctorate
position in nutritional biochemistry and laboratory science at Metametrix (now Genova) Clinical
Laboratory under the direction of Richard Lord, Ph.D. Her residency was completed at
Progressive Medical Center, a large, integrative medical practice in Atlanta, Georgia. Dr.
Fitzgerald is lead author and editor of Case Studies in Integrative and Functional Medicine, a
contributing author to Laboratory Evaluations for Integrative and Functional Medicine and the
Institute for Functional Medicine’s updated Textbook for Functional Medicine. She has been published in numerous peer-
reviewed journals. Dr. Fitzgerald is on faculty at the Institute for Functional Medicine, and is an Institute for Functional
Medicine Certified Practitioner. She is a clinician researcher for The Institute for Therapeutic Discovery. Dr. Fitzgerald
regularly lectures internationally for several organizations and is in private practice in Sandy Hook, Connecticut.
Romilly Hodges completed her Master’s degree in Human Nutrition at the University of Bridgeport,
CT. She is a Certified Nutrition Specialist through the Board for the Certification of Nutrition
Specialists, and completed her practice hours under the supervision of Dr. Deanna Minich, PhD
and Dr. Kara Fitzgerald, ND. She has published in the Journal of Nutrition and Metabolism on
food-based modulators of detoxification enzymes, and has been a contributing author to Sinatra &
Houston, Nutritional and Integrative Strategies for Cardiovascular Medicine. She has been
teaching assistant to Dr. Minich for the Certified Food and Spirit Practitioner Program and the Food and Spirit Advanced
Detoxification Module. She is the staff nutritionist at the office of Dr. Kara Fitzgerald where she advises and supports
patients in the implementation of complex, multi-layered dietary and nutritional protocols that are uniquely personalized to
each individual’s needs.
© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 2

All contents copyright © 2016 by Kara Fitzgerald, ND. All rights reserved. No part of this document or the related documents may be reproduced or
transmitted in any form, by any means (electronic, photocopying, recording, or otherwise) without the prior written permission of the publisher.
Disclaimer: No publication can be assumed to encompass the full scope of information that an individual practitioner brings to his or her practice and,
therefore, this book is not intended to be used as a clinical manual recommending specific treatments or tests for individual patients. It is intended for
use as an educational tool, to broaden the knowledge and perspective of the practitioner. It is the responsibility of the healthcare practitioner to make
his or her own determination of the usefulness and applicability of any information contained therein. If medical advice is required, the services of a
competent professional should be sought. The final decision to engage in any medical treatment should be made jointly by the patient and his or her
healthcare practitioner. Neither authors assume any liability for any errors or omissions or for any injury and/or damage to persons or property arising
from the use of information to be found in this publication.

TABLE OF CONTENTS
1 Abbreviations ..........................................................................................................................................................6
2 Preface: The Need For Conservative Yet Effective Methylation Support .......................................................8
3 Introduction ...........................................................................................................................................................11
4 An Introduction to Methylation ..........................................................................................................................14
4.1 The Biochemistry of Methylation ..........................................................................................................14
4.2 Endogenous Methylation Uses ..............................................................................................................15
4.3 DNA Methylation Plasticity ..................................................................................................................17
5 The Clinical Problem ............................................................................................................................................19
5.1 Methylation Deficits................................................................................................................................19
5.2 Folic Acid Concerns ................................................................................................................................22
5.3 Methyl Donor Intolerance ......................................................................................................................23
5.4 Methylation Gone Awry ........................................................................................................................25
5.5 Reason to Tread Carefully......................................................................................................................32
6 Assessment of Methylation Status ......................................................................................................................33
6.1 Genetic Profiling ......................................................................................................................................33
6.2 Nutrient status .........................................................................................................................................37
6.3 Methylation Metabolites ........................................................................................................................41
6.4 Nutrient Assimilation Capability..........................................................................................................43
6.5 Inflammation ...........................................................................................................................................43
6.6 Oxidative Stress .......................................................................................................................................44
7 The Methylation Diet and Lifestyle ....................................................................................................................46
7.1 Food-Based Nutrients .............................................................................................................................47
7.2 Support for Nutrient Assimilation ........................................................................................................51
7.3 Microbiome ..............................................................................................................................................52
7.4 Inflammation ...........................................................................................................................................53
7.5 Oxidative Stress .......................................................................................................................................54
7.6 Detoxification ...........................................................................................................................................55
7.7 Stress Management .................................................................................................................................57
7.8 Exercise .....................................................................................................................................................58
7.9 Nutraceutical Interactions ......................................................................................................................60

7.10 Medication Interactions ..........................................................................................................................61

8 The Methylation Diet Food Plan .........................................................................................................................63
9 Menu Plans.............................................................................................................................................................71
9.1 Sample Menu 1: Gluten-Free, Dairy-Free ............................................................................................71
9.2 Sample Menu 2: Paleo.............................................................................................................................72
9.4 Menu Nutrient Analyses ........................................................................................................................73
10 RECIPES ............................................................................................................................................................74
Breakfast ................................................................................................................................................................75
Lunch .....................................................................................................................................................................85
Dinner ....................................................................................................................................................................96
Side Dishes ..........................................................................................................................................................106
Snacks...................................................................................................................................................................114
Smoothies & Juices .............................................................................................................................................121
11 Appendix A: Checklist for Methylation Assessment ................................................................................128
12 Appendix B: Checklist for Methylation Interventions ..............................................................................129
13 References .......................................................................................................................................................130

1 ABBREVIATIONS
AHYC Adenosyl homocysteinase

AGE Advanced glycation end-product
AIP Autoimmune pancreatitis
ALU Arthrobacter luteus
ATP Adenoise triphosphate
ADD Attention deficit disorder
ADHD Attention deficit hyperactivity disorder
Bcl-2 B-cell lympoma 2
BHMT Betaine homocysteine methyltransferase
BH2 Dihydrobiopterin
BH4 Tetrahydrobiopterin
BMI Body mass index
BMPRII Bone morphogenetic protein receptor 2
CBS Cystathionine beta-synthase
CDC Centers for Disease Control and Prevention
CIDP Chronic inflammatory demyelinating polyneuropathy
COMT Catechol-O-methyltransferase
CoQ10 Ubiquinone or coenzyme Q10
CpG C: Cytosine triphosphate deoxynucleotide p: phosphodeister, G:
guanine triphosphate deoxynucleotide
CRP C-reactive protein
DFE Dietary folate equivalents
DHA Docosahexaenoic acid
DHF Dihydrofolate
DHFR Dihydrofolate reductase
DNA Deoxyribonucleic acid
DNMT Deoxyribonucleic methyltransferase
EGCG Epigallocatechin 3-gallate
Fli-1 Friend leukemia integration 1 transcription
FODMAPs Fermentable Oligo –Di- Monosaccharides and Polyols
FR Folate receptor
GI Gastrointestinal
HPA axis Hypothalamic-pituitary-adrenal axis
HVA Homovanillate
IgE Immunoglobulin E
IL Interleukin

KLF5 Kruppel-like factor 5

L-Dopa Levodopa or L-3,4-dihydroxyphenylalanine
MBP Mega base pair
5-mC 5-methylcystosine
5-hmC 5-hydroxymethylcystosine
MAO Monoamine oxidase
MAT Methionine adenosyltransferase
MDL Methylation Diet and Lifestyle
MS Methionine synthase
MST1 Macrophage stimulating 1
MTFHR Methylene tetrahydrofolate reductase
MTHF Methyltetrahydrofolate
MTRR Methyl tetrahydrofolate-homocysteine methyltransferase
reductase
MTR Methyl tetrahydrofolate-homocysteine methyltransferase
MTases SAMe dependent methyltransferases
NK Natural killer
NRF2 Nuclear factor erythroid 2 [NF-E2]-related factor 2
NFkB Nuclear factor kappa-B
NHANES National health and nutritional examination survey
NLRP3 Nod-like receptor protein 3
8-OHdG 8-hydroxy-2’-deoxyguanosine
PABA Para-aminobenzoic acid
POP Persistent organic pollutants
RBC Red blood cell
REST RE1-silencing transcription factor
RNA Ribonucleic acid
SNP Single nucleotide polymorphism
SAH S-adenosyl homocysteine
SAHH S- adenosyl homocysteine hydrolase
SAMe S-adenosyl methionine
SIBO Small intestine bacterial overgrowth
SAHH S-adenosyl-L-homocysteine hydrolase
TET Ten-eleven translocation
TNF Tumor necrosis factor
UMFA Unmetabolized folic acid, sometimes referred to as folic acid,
synthetic folate or oxidized folate
VMA Vanilmandelic acid

2 PREFACE: THE NEED FOR CONSERVATIVE YET EFFECTIVE

METHYLATION SUPPORT
From the desk of Dr. Kara Fitzgerald, ND
With the mapping of the human genome in 2001, the era of Systems Medicine has burst forth.
At about 24,000 genes, the code for our lives was smaller than expected (you’ve no doubt heard
the humorous comparison: “less than a grape, but more than a chicken”). Significant attention is
now being paid to the regulatory aspects of the genome, and research on the heritable
epigenome in particular is galloping ahead. At this writing, a PubMed search on
“methylation”—a cornerstone epigenetic and metabolic process—yields more than 85,000 hits.
Many genetic methylation research abstracts are summarized with the preface statement, “For
the first time ever, we’ve shown that…”
With rapidly emerging understandings, and ready access to genetic testing, it is indeed a wildly
exciting time to be practicing Functional Medicine, the clinical application of Systems Medicine.
Many of our patients now arrive at our offices with some knowledge of their genetics, and most
often with regard to their single nucleotide polymorphisms (SNPs) relating to methylation.
Many assumptions are made around the phenotypic expression of these single nucleotide
variations. Last week, a new patient sat before me, stating with grim determinism that her
heterozygous mutation in MTHFR A1298C SNP made it impossible for her body to detoxify
efficiently.
To those of us looking for biochemical “lesions” in methylation enzymes using a combination of
genetic testing and the currently available metabolic biomarkers they appear to be common...
Sometimes correcting identified imbalances can be highly clinically significant, other times
(arguably more often than not) shifting biochemical methylation activity with high-dose methyl
donors such as folate and B12 doesn’t appear to have a huge, immediate clinical outcome. But
we know that methylation is incredibly fundamental and operates in many “behind the
scenes” activities not limited to detoxification, neurotransmitter production and of course the
all-important black box of epigenetic regulation. We’ve seen the powerful impacts of folic acid
fortification in the reduction of neural tube defects, where augmenting methylation activity is a
piece of the folic acid success story.
The spark of inspiration behind creating the Methylation Diet and Lifestyle (MDL) program
was wanting to “do right by my patients” by embracing both the importance of healthy
methylation balance while recognizing the limitations of our current understanding. What
we don’t know in the biological sciences always far outweighs what we do know, and this is
especially true in our understanding of methylation. Imbalanced methylation of the epigenome
(comprising both hyper- and hypomethylation primarily of gene promoter regions) is an

emerging area of investigation implicated in many disease processes, ranging from aging and
allergies to neurodegenerative processes and cancer. Regulation of the epigenome is a highly
complex process; we cannot state with certainty what the impact is of high-dose, long term
methylation interventions.
Thus, for the vast majority of our patients we need to consider whether high-dose, long-term
supplementation really is the right approach. There is a dearth of research in this area, with
the exception of folic acid, where, as we discuss below, reasonable concerns exist. There are also
those patients who do not tolerate methyl donor supplementation, suspected to be chiefly due
to either poor clearance of epinephrine and other biogenic amines, or “ramped up”
detoxification activity.
While homage to Dr. Bruce Ames and his remarkable work around increasing enzyme kinetics
using high dose cofactor supplementation is due, and understanding that this approach may
indeed be appropriate for methylation in the short-term, our emerging understanding on the
epigenome suggests that more “up-stream” and nuanced interventions are in order when
possible. Food-based folates, for instance, have only been shown to be protective. Numerous
additional phytochemicals, not directly tied to methylation, appear to favorably modulate
global epigenetic and biochemical methylation activity. And reducing methyl donor depletion
by minimizing toxic exposures, nourishing the microbiome, augmenting the stress response and
far more, is safe and impactful. By removing the obstacles and drains on methylation while
providing broad spectrum nutrient ingredients for balanced activity, we are allowing
physiological wisdom to manage the process.
The Methylation Diet and Lifestyle would not have been brought into being in my clinical
practice or in this eBook without the years of frank discussions I’ve had with leading expert
Michael Stone, MD on current research and patient care approaches1. Likewise with my Journal
Club comrades, where each month for over the last three years we meet and “tussle with” new,
often complex concepts in the biological sciences. A heart-felt “shout out” goes to my
nutritionist extraordinaire, Romilly Hodges, who has worked tirelessly with me to capture the
bulk of our thoughts in the below text.
This eBook serves as a guide to understand the current methylation issues and challenges facing
practitioners, the potential concerns with supplementation alone, how to assess methylation
1Drs. Leslie and Michael Stone, along with their daughter, nutritionist Emily Rydbom, are doing
remarkable work in the field of methylation assessment and support during preconception, pregnancy
and the postnatal period at their clinic in Ashland, Oregon. Find them at www.ashlandmd.com and
www.growbabyhealth.com.

status, and how to incorporate an MDL program into your protocols. Not only are there easy-
to-apply menus, recipes and nutrient guidelines but important lifestyle factors are reviewed
as well.
How should we determine when to use the MDL? Well, it may be the optimal way to offer
methylation support right off the bat, especially for those who cannot tolerate
supplementation. It is also a sensible and safe long-term strategy for most patients who have
achieved balance through a short-term course of higher-dose methyl donors. Importantly, the
full MDL program also supports detoxification, stress reduction, microbiome and hormone
balance, and can be readily modified to incorporate other programs that we routinely prescribe
such as elimination diets, grain and lectin-free plans, low FODMAP diets and general gut
restoration programs. Highly restricted plans, such as the calorie restricted ketogenic diet,
sometimes used in cancer and epilepsy, can incorporate aspects of the methylation diet with
additional nutraceutical support. Virtually any dietary program can work with the MDL as a
foundation.
Acknowledgements
We would like to acknowledge P. Michael Stone, MD, MS,
Institute for Functional Medicine, for his groundbreaking work in
the area of methylation.
We would also like to thank Lara Zakaria MS for her
contributions to the menus, recipes and figures, and Brigid Krane
(www.brigidkrane.com) for the cover and logo design.

3 INTRODUCTION
It has become increasingly common for functional medicine practitioners to recommend high-
dose supplementation with methyl donors, such as 5-methyltetrahydrofolate (5-MTHF) and
methylcobalamin, in certain patients. For example in those with genetic polymorphisms that
may impair the functionality of relevant enzymes, most commonly methylenetetrahydrofolate
reductase (MTHFR), or in those with out-of-range methylation-related biomarkers such as in
hyperhomocysteinemia. Deficiency in methyl donors is a fairly frequent finding in laboratory
analyses, depending on your population, and can relate directly to clinical symptoms; for
example B12 deficiency-associated neuropathy, which is relatively common. Some practitioners
may even look to supporting methylation as a means to improve inherited or environmentally
acquired epigenetic programming.
Of course, improving global methylation status and averting the pathways of disease and
dysfunction associated with a potential deficit in methylation activity is a commendable goal.
However, as with other biochemical processes, methylation activity exists ideally in a state of
active balance, or homeodynamics. Imbalance in these mechanisms can lead to dysfunction and
disease. So while we can be confident that ensuring the adequacy of available methyl donors for
use in the body is important, we have to question whether “pushing” reaction rates using
supraphysiological doses is always safe. Rather than bluntly forcing reactions forward, perhaps
our ultimate goal should instead be enabling the body to do the right thing at the right time.
There are a number of potential issues with long-term high-dose methyl-donor
supplementation:
The impact of genetic alterations is unclear. Aside from the altered activity of MTHFR C677T
and A1298C single nucleotide polymorphisms (SNPs) which has indeed been studied to some
degree, the discovery of other SNPs remains a qualitative rather than quantitative indicator of
enzyme functionality. The overall effect of these SNPs on methylation depends on the activity
of many enzymes working together in the context of one’s internal and external environment.
This fact underlies the many variable results found in genome-wide association studies. As a
result, it isn’t readily possible at this time to determine exactly how much of an impact any one
of those alterations, even MTHFR C677T, has on overall methylation status [1].
The correct supplementation dose is as yet unknown, and may vary between individuals. No
studies have clarified yet what the right dosage or duration of methyl donor supplementation is
needed to rebalance biochemical or epigenetic methylation status Some side effects of high-dose
5-methyltetrahydrofolate supplementation have been reported in clinical practice, including
worsening of symptoms and anxiety. Consequently it may be safer in the long term to stay
within physiologic levels [2].

Hypermethylation states may occur and may also be detrimental: The scientific literature
contains many examples of region-specific DNA hypermethylation associated with adverse
outcomes, including cancer, immune dysfunction and Downs Syndrome. Interestingly, both
DNA hyper- and hypomethylation states can be identified in states of methyl donor deficiency
and repletion. Certainly folic acid, in either deficiency or excess, has been associated with
increased rates of cancer and immune hypersensitivity, but since the mechanism is not fully
understood, should we not also be cautious with high levels of methylated folate? The
mechanisms controlling DNA methylation and demethylation are incredibly complex, yet we
know that pushing reaction rates through supraphysiological dosing of nutrient cofactors is
possible [3]. The bottom line is that we don’t know what effect long-term, high-dose methyl-
factor supplementation has on DNA methylation.
Methylation status depends on many dietary and lifestyle inputs: A complex interaction of
dietary and lifestyle factors (including medications, stress, sleep, exercise and toxin exposure)
plays a role in the methylation end-result. Singular interventions with high dose nutrient
supplementation miss this intricate web of inputs and may lack long-term effectiveness, or may
not achieve desired results.
Dietary and lifestyle interventions may be the best, and safest, long term option for most
individuals with suspected methylation imbalances. This may be particularly true for certain
vulnerable populations such as individuals with active cancers. Aging is known to be associated
with diminished methylation activity, so there is a good rationale for using the MDL as an anti-
aging tool. Careful methylation evaluation and treatment is essential during preconception,
pregnancy and the postnatal period2. A good evaluation coupled with the MDL program and
appropriate nutraceutical support is a useful starting place.
A dietary and lifestyle approach can also be used as a long term follow-up plan to those
requiring early high-dose nutraceutical support. Food sources of methylation nutrients can be
abundant, and with proper planning, dietary modifications have been found to favorably
influence methylation activity [4], [5].
In this eBook, you’ll find a comprehensive dietary and lifestyle approach to support
methylation, aligned with a functional medicine approach and including important methylation
nutrients, specific foods to include, foods to avoid, two 7-day menu plans (with calculated
2
Drs. Leslie and Michael Stone, along with their daughter, nutritionist Emily Rydbom, are doing
remarkable work in the field of methylation assessment and support during preconception, pregnancy
and the postnatal period at their clinic in Ashland, Oregon. Find them at www.ashlandmd.com and
www.growbabyhealth.com.

levels of methylation nutrients), recipes and lifestyle factors. You’ll also learn the basic
biochemistry of methylation, the many roles of methylation in the body, how to assess patient
methylation status, the beneficial and potentially detrimental clinical impacts of supplemental
methyl donor interventions, and the potential issues with too little, or too much methylation
activity.

4 AN INTRODUCTION TO METHYLATION
4.1 THE BIOCHEMISTRY OF METHYLATION

Methylation, also commonly termed “one-carbon metabolism,” is a biochemical process that
involves the transfer of active methyl groups. Methyl groups consist of a hydrogen attached to
three carbons (-CH3) and can be formed in two ways:
1. By the addition of a hydrogen ("reduction”) to methylene (-CH2-) groups, such as is

facilitated by the enzyme methylenetetrahydrofolate reductase (MTHFR).The product of
this reaction is 5-methylTHF.
2. By the transfer of a complete methyl group, such as is done by catechol-O-
methyltransferase (COMT) or DNA methyltransferase (DNMT) enzymes [6].
Methyltransferase enzymes use methyl groups donated from the universal active methyl
transfer compound S-adenosylmethionine (SAMe).
As it is utilized, SAMe is converted to S-adenosyl homocysteine (SAH), and then homocysteine
(Figure 1). Homocysteine recycling to methionine can occur via one of two pathways. The
dominant pathway, via methionine synthase conversion, requires the transfer of a methyl group
from 5-methyltetrahydrofolate (5-mTHF). 5-mTHF is formed, irreversibly, by the enzyme
methylenetetrahydrofolate reductase (MTHFR), perhaps the most widely-known of all enzymes
in the folate metabolic pathways.
A lesser pathway for methionine biosynthesis from homocysteine is via betaine homocysteine
methyltransferase in the liver and kidney. Homocysteine may also enter another biochemical
pathway, especially during states of higher oxidative stress, which converts homocysteine to
cystathionine and from there to taurine, glutathione or sulfate. The first step in transulfuration
pathway is irreversible, however, glutathione recycling may spare homocysteine for SAMe
production.
Dietary folate is found in foods primarily as pteropolyglutamates. In order to be absorbed, the
polyglutamate form is hydrolyzed in the intestines to the monoglutamate form,
tetrahydrofolate (THF).
Folic acid on the other hand, the most common synthetic form of the vitamin (and the form
used in food fortification), must be reduced by the enzyme dihydrofolate reductase (DHFR)
twice (i.e. it requires the addition of two hydrogens) in the liver before it can enter folate cycles
as THF. Importantly, it is known that DHFR activity is low and variable [7]. Human liver DHFR
activity is also 56 times slower per gram of tissue than in the rat, meaning that we should use
caution when translating the pharmacokinetic studies of folic acid in animals [8].

Figure 1: Methylation Pathways and Utilization (for enzyme cofactors and allosteric activators see Figure
4)
Oftentimes, functional medicine practitioners will use other forms of supplemental folates
including 5-mTHF and folinic acid (10-formyl THF) to avoid the potential DHFR blockage, and
in the case of 5-mTHF with the intention to bypass polymorphism blockages at the MTHFR
enzyme. Studies comparing the effects of 5-mTHF versus folic acid on folate status have found
the natural, methylated form to be at least as effective at raising folate levels [9]. Folinic acid is
sometimes used since it appears able to support cerebral folate levels in specific circumstances
where autoantibodies to folate transport proteins at the blood brain barrier are present [10].
4.2 ENDOGENOUS METHYLATION USES

The production of methyl donors is essential for a number of fundamental and critical
biochemical pathways. An understanding of their known uses provides an irrefutable argument
for the need to ensure effective methylation in the body.

Cell division, DNA and RNA synthesis. Folate metabolism is critical for DNA and RNA
synthesis since it is involved in the biosynthesis of purine nucleotides and thymidylate [11].
Chronic methyl deficiency increases the potential for cytosine deamination to uracil, creating
mismatch gene sites which increase the risk for DNA strand breaks, fragmentation, apoptosis
and carcinogenesis [12].
Early CNS development. It has been known since the 1960s that folate deficiency is causatively
associated with increased risk for neural tube defects [13]. The mechanism for this has yet to be
fully elucidated, and although there are likely multiple genetic and environmental influences.
Methylation imbalance is one suspected factor [11]. National folic acid food fortification
programs have been successful at reducing the incidence of this condition in newborns [14].
Gene expression. DNA and histone methylation are major epigenetic mechanisms that regulate
the expression of genes. The most common mechanism of DNA methylation is the attachment
of a methyl group to cytosine bases in CpG dinuceotides by DNA methyltransferase (DNMT)
enzymes [15]. Up to 80% of CpG dinucleotides are methylated in mammals under normal
conditions. High levels of methylation in gene promoter regions typically lead to repression.
Histone methylation can either promote or repress expression. Research suggests that aberrant
promoter hypermethylation in DNA repair genes is linked to a variety of cancers [16], [17].
Post-transcription modification. Methylation of post-transcription RNA and microRNA
appears to act in a regulatory function on microRNA translation and protein synthesis.
Aberrant RNA methylation activity is starting to be understood to correlate with myriad disease
states [18].
Immune cell differentiation. Methylation is involved in the maturation of immune cells such as
T cells (including Th2 cytokine regulation) and natural killer cells [19].
Neurotransmitter biosynthesis and metabolism. Methylation via SAMe is a key step in the
synthesis and metabolism of biogenic amine neurotransmitters, including dopamine,
norepinephrine, epinephrine, and serotonin. It is also required in the pathway for acetylcholine
biosynthesis. Methylation is also necessary for the regeneration of tetrahydrobiopterin, another
important cofactor in these biosynthetic pathways.
Histamine clearance. One pathway for histamine metabolism is via histamine N-
methyltransferase, requiring SAMe as methyl donor. Low SAMe or altered enzyme activity can
lead to an increases accumulation of histamine and clinical symptoms [6].
Detoxification. Along with glucuronidation, sulfuration, and acetylation, methylation is a
major pathway for biotransformation of xenobiotics within phase II detoxification. Poor
methylation status can therefore impair the body’s ability to detoxify and can lead to toxicity-
related dysfunction. Separately, DNA methylation also regulates Nrf2 signaling, referred to as

“the master regulator of antioxidant defense” a key mechanism that upregulates various phase
II detoxification enzymes [20].
Hormone biotransformation. The methylation of estrogens via COMT is an important
mechanism for their clearance and regulation. The interruption of this mechanism can be one
factor in the increased risk for oxidative DNA damage from certain estrogen metabolites [21].
Methylation status is therefore an important consideration to support safe estrogen clearance
and detoxification in patients presenting with estrogen dominance or with estrogen-receptor
positive cancers.
Cellular energy metabolism. Through its role in the biosynthesis of CoQ10, carnitine and ATP,
methylation plays a critical role in mitochondrial energy metabolism in every cell [6].
Phospholipid synthesis. SAMe is required for the biosynthesis of phosphatidylcholine, a major
component of cellular membranes and acetylcholine precursor [22].
Myelination of peripheral nerves. Deficient concentrations of SAMe in cerebrospinal fluid
have been shown to be causative in demyelination [23].
4.3 DNA METHYLATION PLASTICITY

Most DNA methylation is highly regulated, leading to little interindividual differences in
epigenetic patterns [24]. However, DNA methylation imprints at regions termed “metastable
epialleles” have been shown to occur stochastically, with significant interindividual differences,
to be passed down to offspring during critical periods of fetal development, and preserved
across multiple generations [24]–[26]. This genetic imprinting has been shown to be highly
sensitive to environmental influences. For example, transient exposure to the fungicide
vinclozolin and the pesticide methoxychlor can induce alterations in DNA methylation patterns
that persist in future generations, despite the lack of continued exposure [26].
It has also been argued that factors that prevent efficient DNMT activity, either by deficiency of
nutrients needed for SAMe biosynthesis or competition for SAMe or DNMT action, during
these sensitive time periods might result in permanent deficits in CpG methylation [27].
Conversely, animal study has shown that maternal supplementation with methylation nutrients
(folic acid, vitamin B12, choline and betaine) during these periods can have a significant,
restorative impact on offspring DNA methylation [24].
Even at other times during life, the preservation of DNA methylation during mitosis in
proliferative tissues may be undermined by nutritional deficiencies affecting methyl donor
status [27] or by inhibition of DNMT activity [28]. In fact, gradual DNA de-methylation occurs
over time, especially between ages 34 to 68, and is assumed to be associated with the normal
aging process [29].

Human investigations support the assertion that non age-associated alterations in DNA
methylation are possible outside of the fetal developmental windows. In a study published in
the Lancet, researchers determined that hyperhomocysteinemia (between 16 and 100 mol/L
plasma or serum) was significantly correlated with DNA hypomethylation in humans (the
population studied aged between 39-68 years) [30]. They theorized this occurred due to the
increase in S-adenosyl homocysteine (SAH), which is a potent competitive inhibitor of SAMe-
dependent methyltransferases (including DNMTs). Induced folate deficiency in the population
studied further worsened hyperhomocysteinemia, and folate treatment (15 mg/d 5-mTHF for 8
weeks) decreased plasma total homocysteine and decreased DNA hypomethylation [30].
More evidence that DNA methylation is modifiable outside the critical development windows
comes from animal studies, with indications that dietary interventions may help to restore
methylation status where it has been previously lost in early-life programming. For example,
methionine supplementation in adult rodent offspring has been shown to reverse DNA
methylation changes in the hippocampal glucocorticoid receptor, as well as the adrenal and
behavioral responses to stress, caused by negative maternal behaviors in early life [31]. And
dietary betaine supplementation in vivo has been shown to induce promoter hypermethylation
on specific genes in porcine liver [32]. Even though the evidence is still limited, and more
research is needed to form strong conclusions, a number of other in vitro, animal and human
studies demonstrate alterations in DNA methylation status that are driven by nutrient
availability, including folate, choline, vitamin B12, and vitamin B6. Intriguingly, and perhaps
most telling, the outcomes of many of these studies suggest that multiple factors such as
lifestyle, environmental exposures and food-based modulators of epigenetic imprints, not just
nutrients, shape the overall impact on DNA methylation outcomes [28], [33], [34].

5 THE CLINICAL PROBLEM
5.1 METHYLATION DEFICITS

The risk of folate deficiency and impaired folate metabolism has been most clearly illustrated by
the association with neural tube defects. Without a doubt, the mandatory folic acid programs
implemented by the majority of developed countries in the last two decades have had a
tremendous, positive impact on the incidence of these conditions [35]. This clear benefit cannot
be dismissed, despite the emerging concerns over the use of synthetic folic acid forms.
Beyond neural tube defects, deficits in folate and methylation status have also (and more
recently) been associated with ADD/ADHD, addiction, allergies, Alzheimer’s Disease, anxiety,
asthma, atherosclerosis, autism spectrum disorder, behavioral changes, bipolar disorder,
cancers, chemical sensitivity, chronic fatigue, cleft palate, diabetes, dementia, depression,
Downs syndrome, essential hypertension, fertility issues, fibromyalgia, insomnia, multiple
sclerosis, neuropathy, Parkinson’s Disease, schizophrenia, and thyroid disease [6], [36]–[38].
Clearly methylation is a critical aspect of physiology, with wide-ranging application, and
demands our clinical attention.
It is recognized that an individual may become deficient in methylation activity in multiple

ways, including via nutrient deficiency, competition for methyl donor utilization, methylation
inhibitors and genotype:
NUTRIENT DEFICIENCY
The depletion of cellular pools of methyl donors due to nutrient depletion can interfere with
both metabolic and DNA methylation activity [39]. There are many nutrients involved in
methylation pathways, which we will cover in more detail below. However, the most
commonly-recognized of these are folate (a B vitamin) and vitamin B12. There are various
factors that can impact the status of these, and other, nutrients in the body.
According to NHANES data, mean US adult dietary intake of food-fortified folic acid and
natural food folates range from 454 to 652 mcg DFE per day, of which 190 mcg/d is estimated to
come from folic acid fortification [40]. This is compared with a target RDA of 400 mcg/d DFE.
Population means for erythrocyte folate levels also fall within so-called sufficient levels,
however certain groups are identified as being at higher risk for deficiency. These include
women of childbearing age and non-Hispanic black women. In our clinic we also routinely see
low levels of dietary folate intake (ranging from 200-350 mcg/d DFE) in incoming patients who
have removed sources of fortified foods from their diet, such as gluten-containing grains and
processed breakfast cereals. While it is clearly advantageous to avoid processed and refined
foods, and avoid provoking food sensitivities where they exist, care must be taken to increase
natural sources of folate to achieve optimal intake levels.

Mean intake for vitamin B12, is estimated at 3.4 mcg/d, higher than the 2.4 mcg/d RDA for most
adults [40]. However, we know that certain population groups are more vulnerable for
functional deficiency. As we age, we have a reduced ability to produce the gastric hydrochloric
acid and intrinsic factor necessary for B12 assimilation. This can be compounded by the
presence of autoimmune pernicious anemia that further limits gastric secretions [22].
Many patients that seek out a functional medicine practitioner also have conditions that can
negatively impact nutrient absorption and the functional status of nutrients in the body,
including dysbiosis, small intestine bacterial overgrowth, altered transit time, Crohn’s disease,
food allergies or sensitivities, impaired thyroid function and more. These should all be assessed
and factored in to the overall nutrient need of the individual.
Ironically, while a move away from processed food-based diets is a clearly essential for
optimizing health, fortification is no longer the ‘catch all’ that it is in the processed food world.
Improperly-implemented whole-food diets still have the potential to be imbalanced. Care must
be taken to include foods that together provide all necessary nutrients, including methylation
nutrients, and it seems wise to also check functional nutrient status through laboratory
evaluations especially in the context of genetic SNPs and/or clinical symptoms.
COMPETITION FOR METHYL DONORS

High demand from any single area of methylation activity outlined above, such as high
catecholamine turnover, detoxification states, histamine clearance, or circulating estrogens, can
drain the pool of available methyl donors.
For example, in states of high physiological and psychological stress, SAMe utilization for
catecholamine biosynthesis and degradation is increased and can impact the availability of
SAMe for other uses. Similarly, in individuals with active, ongoing reactivity to antigens, high
histamine turnover can place significant demands on methyl donor levels.
L-Dopa medication is a common therapy in patients with Parkinson’s disease. L-Dopa
metabolism occurs via COMT with SAMe as a cofactor that donates its methyl group, and its
use is associated with reduced plasma folate and elevated homocysteine [41]. It is not without
irony that L-Dopa may therefore compromise the very methylation detoxification capacity that
can remove the heavy metals and other toxins that can be significant, causative contributors to
the condition.
METHYLATION INHIBITORS
S-adenosyl homocysteine (SAH) is a powerful competitive inhibitor of SAMe-dependent
methyltransferases (including DNMT), and is often increased with hyperhomocysteinemia [30].
The conversion of SAH to homocysteine is catalyzed by S-adenosyl homocysteine hydrolase, is
fully-reversible, and favors biosynthesis rather than hydrolysis [30]. Therefore, an accumulation

of homocysteine can inhibit hydrolysis and promote formation of SAH, thereby inhibiting
SAMe-dependent methylation activity.
GENOTYPE
Even though the MTHFR SNP may have landed methylation ‘on the map,’ there are many
enzymes and their corresponding genes that play a role in overall methylation status and
clinical outcomes. A number of practitioners already incorporate genotyping into their patient
assessment. In addition, patients are able to order genetic profiling on their own, and are
starting to bring that data to their health practitioners for evaluation and advice.
Frequency and effects of MTHFR polymorphisms

The most common MTHFR polymorphisms are C677T and A1298C. The frequency of
homozygote 677TT variants is highly variable according to ethnicity and geography. The
highest frequency (>20 percent) is reported in US Hispanics, Colombians and Amerindians in
Brazil. The frequency among White populations in Europe, North America and Australia is 8 –
20 percent. The lowest frequency (<2 percent) is found in Black populations. The frequency of
homozygote 1298CC genotypes in White populations in North America and Europe is reported
to be 7-12 percent. Lower frequencies are reported in Hispanics (4-5 percent) and Asian (1-4
percent) populations. [42]. Clear data are lacking as to the dispersion of heterozygote
genotypes, as well as compound genotypes, among population groups.
Of potential clinical relevance, it appears that the incidence of C667T polymorphisms may be
increasing: Population studies from Spain, for example, report an increasing frequency of the
C677T genotype in the post folic acid-fortification era. This is speculated to be due to the
decreased levels of spontaneous abortions that are more likely when the polymorphism is
present in conjunction with low folate status [43].
We know that these genetic polymorphisms alter enzyme capacity and stability. Homozygous
667TT variants have been found to have a 70-75% loss of enzyme activity [44], [45].
Heterozygotes appear to lose 33-35% of enzyme activity [44], [45]. Homozygous 1298CC
genotypes appear to have a 39% reduction in enzyme activity, and heterozygotes a 17%
reduction [45]. Compound heterozygotes for both 667CT and 1298AC may also lose as much as
52% of enzyme activity [45].
In turn, research also shows that this change in enzyme capacity does have an effect on blood
folate concentrations and homocysteine levels. A recent systematic review and meta-analysis
reports a 16% decrease in erythrocyte folate levels for homozygous 677TT genotypes when
compared with their wildtype 677CC counterparts [46], and an 8% decrease for heterozygous
677CT genotypes. Note that red blood cell folate measurements include all the different folate
vitamers, so we cannot separate out the effect of these genotypes on 5-mTHF, the active form
needed for homocysteine metabolism.

AGING
Aging is associated with altered DNA methylation, specifically global hypomethylation but
with hypermethylation at normally unmethylated CpG regions, which may lead to the
suppression of specific genes or genomic instability [28], [29]. Preserving methylation status via
nutrient and lifestyle support may be considered a reasonable strategy to slow the age-related
decline in methylation status.
5.2 FOLIC ACID CONCERNS

Fortification and regular folic acid supplementation are now strongly suspected to carry risks,
despite their clear benefits in preventing neural tube defects, especially at levels above the
recommended intake of 400 mcg/d of dietary folate equivalent units (DFEs).
Folic acid is a purely synthetic compound that in itself has no known cofactor role. To be used
in methylation pathways, it must be first converted to tetrahydrofolate (THF) by being twice-
cycled through the enzyme dihydrofolate reductase (DHFR). One suspected cause of adverse
folic acid effects is elevated unmetabolized folic acid (UMFA) due to the inefficiency of this
mechanism and distinctly limited capacity of liver DHFR, now proposed to be the major site of
folic acid metabolism [8]. One-time doses of about 260 mcg folic acid, or even multiple 100 mcg
doses throughout the day have been shown to lead to detectable UMFA in serum [7].
Populations who regularly consumer fortified foods such as ready-to-eat cereals as well as
fortified grains can have a folic acid exposure up to the Tolerable Upper Limit of 1.0 mg/d, and
with the use of multivitamin supplements, it is not uncommon for intake to rise beyond that [8],
[43], [47], [48].
Another essential consideration is that folic acid from supplements is much more readily
absorbed than folate from foods. In fact, one DFE is equivalent to 1 mcg of dietary folate but
only 0.6 mcg folic acid from supplements (taken with food) or fortified foods [49]. Therefore 400
mcg of folic acid from a supplement should actually be considered as 667 mcg DFE.
Several studies link higher levels of folic acid intake with adverse health outcomes. This has led
to speculation that dihydrofolate (DHF), an intermediate metabolite in the conversion of folic
acid to tetrahydrofolate, and UMFA, may have deleterious effects.
Reported effects of DHF: DHF has been shown to inhibit thymidylate synthase and purine
synthesis enzymes, which has the potential to impair DNA synthesis [43]. DHF also appears to
inhibit the MTHFR enzyme, creating a “pseudo MTHFR deficiency,” which can ironically lead
to a decrease in methionine synthesis and homocysteine clearance [43], [50]. Perhaps this is why
a recent trial of high-dose (5 mg/d) folic acid supplementation in infertile men showed an
unexpected reduction in sperm DNA methylation, an effect that was most pronounced in
patients homozygous for the MTHFR C667T polymorphism [51].

Reported effects of UMFA: Various studies have also reported a connection between folic acid
fortification and supplementation and colorectal cancer [52]–[55]. One of the proposed
mechanisms is that UMFA may actually metabolize via photo-catalysis to DNA-toxic products
[55]. A recent study that investigated the potential connection between levels of prediagnostic
UMFA and subsequent colorectal cancer diagnosis found a small positive association in men
and individuals with MTHFR C677T genotype (both heterozygous and homozygous) with the
highest levels of plasma UMFA as compared to those with no observable plasma UMFA.
However, a small inverse association was found with women in the study [56]. Higher UMFA
was also found to be associated with anemia in US seniors who consumed alcohol, and reduced
NK cell cytotoxicity in otherwise healthy postmenopausal women [56].
Recent research looking at folate receptors in epithelial cancers found a high frequency of
receptor FR-alpha which preferentially uptakes UMFA. It is believed that FR-alpha promotes
tumor progression and reduces apoptosis through increased expression of anti-apoptotic
protein Bcl-2, among other mechanisms. Folic acid exposure to tumor cells in-vitro was shown
to enhance this process [57], [58].
5.3 METHYL DONOR INTOLERANCE

Functional medicine practitioners who have been using high-dose methyl donor
supplementation in their patients with indicated methylation deficits, will likely have
encountered individuals who do not feel well on such a protocol. Clinical experience indicates
that a worsening of symptoms, or the appearance of neurological symptoms, or both are
possible outcomes, such that the individual is unable to tolerate the intervention despite a clear
need for methylation support. Neurological symptoms may include heightened anxiety,
irritability, brain fog, or depressed mood.
The mechanism behind these clinical responses is not well understood and there is a need for
research to validate and help clarify the frequency and mechanisms of these effects. It has been
theorized that impaired metabolism of catecholamines via COMT and MAOA may play a role
(Case 1.0). Increased SAH is also thought to be a potential mediator of adverse effects.

Case 1.0: Methyl donor intolerance with COMT polymorphism
31-year-old female with long-term panic disorder and recent onset of agoraphobia. Genetic
testing revealed homozygous for COMT and MTHFR single nucleotide polymorphisms
(SNPs). Vanilmandelic acid (VMA) and homovanillate (HVA) urinary organic acids were low
and low-normal, respectively, indicating poor clearance of norepinephrine and epinephrine.
These catecholamines are catabolized via COMT methylation, and their poor clearance may
contribute to heightened anxiety symptoms. Her homocysteine levels, on the other hand were
normal, suggesting that either the MTHFR SNP was still functional enough to sustain SAMe
levels, or that increased oxidative stress was confounding the normal homocysteine finding, by
increasing transulfuration of homocysteine for glutathione formation.
Supplementation with high-dose methylated folate and betaine was initiated, but soon after the
patient reported an exacerbation of symptoms. This could have been due to the increased
production of SAMe from the combined effects of the supplementation. SAMe levels in the
brain govern the rate of epinephrine biosynthesis from norephinephrine via methylation, so
increased SAMe availability could have been driving increased epinephrine synthesis. This
combined with the decreased clearance due to the COMT SNP could have been the underlying
reason for increased symptomatology. Replacing methylated folate with unmethylated folic
acid, and discontinuation of betaine resulted in significant symptom improvement, including
resolution of the agoraphobia.
Case adapted with permission from Lord & Bralley, 2012, Case Illustration 11.1 p. 594.

5.4 METHYLATION GONE AWRY

5.4.1 Potential concerns about folic acid AND methyl-folate supplementation.
Some of the risks of folic acid or other folate derivatives, including commonly used alternatives
such as 5-mTHF and folinic acid, are widely accepted, and not generally disputed. These are:
- High intake may mask a B12 deficiency. B12 deficiency is normally indicated by
megaloblastic anemia, but in when folate levels are high enough cell division will
continue in bone marrow, and this will mask the anemia. Unaddressed B12 deficiencies
can lead to irreversible neurological damage and cognitive impairment [43], [55].
- Supplemental folate or folic acid may also reduce the efficacy of certain antifolate drugs
such as methotrexate, anticancer, antimalarial and antibacterial medications.
These issues are typically addressed by simultaneous, balanced B12 supplementation and risk-
benefit analysis, respectively, and although important are not the main focus of our discussion
here. What is worth our serious exploration is this: whether or not the adverse effects of folic acid
supplementation, or aberrant DNA methylation activity seen in certain disease states, are a result of
pushing methylation activity too far. Certainly epidemiological data suggest an inverse association
between folate status and risk of disease, however this is not uniformly the case, and some
intervention trials have suggested that excessive methylation factors may in some cases be
harmful. To investigate this perhaps uncomfortable and controversial possibility, we take a
closer look at the literature.
UNEXPLAINED ADVERSE EFFECTS MAY BE DUE TO ABERRANT METHYLATION WHICH

IS NOT NECESSARILY RESOLVED WITH 5-MTHF
Firstly, there are more associations between folic acid supplementation and adverse outcomes
that are not explained by UMFA or DHF (nor yet by any other mechanism), and for which we
cannot rule out the possibility of aberrant or excessive methylation as a contributing/
underlying factor:
IMMUNE DYSREGULATION AND DYSFUNCTION

Epigenetics are known to play a role in the development of allergic disease. For example,
epigenetic changes including DNA hyper- and hypomethylation is associated with childhood
IgE-mediated food allergy [59]. Although not all studies agree about the outcomes and specific
mechanisms, there are findings linking the intake of methyl donor compounds with disease
outcomes that should prompt concern and deeper investigation.
Some research has linked folic acid intake during pregnancy with an increased risk for allergic
disease in offspring [60]. Higher levels of maternal folic acid supplementation (>500 mcg/d vs
<200 mcg/d) have been associated with an 85% increased risk for allergic eczema, for example
[61]. In animals, maternal supplementation with a combination of folic acid, vitamin B12,

choline, L-methionine, zinc and betaine during pregnancy enhances the development of many
features of allergic airway disease including airway hyperreactivity and higher concentrations
of serum IgE [62]. Similar maternal supplementation with non-dietary methyl donors, including
synthetic folic acid, has been shown to increase offspring susceptibility to inflammatory bowel
disease [63]. Another study, not of maternal intake, found that intakes of folic acid above 600
mcg/d (from food and supplements) was associated with impaired Natural Killer cell activity
[43].
BLOOD SUGAR DYSREGULATION

Maternal folic acid supplementation at 500 mcg/d has also been associated with increased
incidence of insulin resistance in children at 6 years of age, an effect apparently exacerbated by
low maternal vitamin B12 status [64], [65].
PRENATAL DEVELOPMENT DYSFUNCTION

High folic acid intake is associated with embryonic loss and growth delay and increased
incidence of ventricular septal heart defects [66].
COMORBIDITY AND MORTALITY IN DIABETIC ADULTS

In a retrospective study of 526 diabetic adults, high levels of RBC folate (determined to be
primarily driven by folic acid intake) were associated with an increased risk for cardiovascular
and cerebrovascular disease [67]. In addition, the hazard ratio for dying within 15 years in those
with the highest levels of RBC folate was 2.10 (95% CI = 1.37 – 3.20), compared with a baseline
(1.00) of those with the lowest levels of RBC folate.
If these unexplained associations between increased methylation factors and disease are caused
via alterations in methylation activity, the possibility exists that alternative forms of folate
supplementation can also alter methylation activity in ways that could generate the same risks.
Unfortunately we simply don’t know enough to rule this out.

“It’s fashionable now to use large doses of methylating agents. But in
that study of Prozac, using 15-50 mg of folic acid in depression, you
have to realize that we have no idea what that is doing to the function
of all the other genes. So if you need to use it for someone who has,
say a mood disorder, use it, but follow the indices and use it for as
short a period as possible.
I used methylated folate to treat a woman with depression. It
happened to cure her endometriosis, too, because endometriosis, in
part, is a genetic methylation defect. So there are places for these
things, but don’t overdo it. Don’t overdo it.”
Robert Hedaya, MD, DLFAPA. Clinical Professor of Psychiatry,
Georgetown University School of Medicine. Faculty, Institute of Functional
Medicine

Changing folate status in humans has been demonstrated to alter DNA methylation [43]. In fact,
one of the outcomes that functional practitioners often assume when they turn to folate
supplements in under-methylating patients is the “restoration” of DNA methylation activity.
Unfortunately, studies about the effect of folate and methylation status on the DNA
“methylome” are conflicting and inconclusive, leaving us to attempt to derive sound clinical
judgment in the absence of hard evidence. We do know that supraphysiological levels of
substrates or cofactors can sometimes serve to override other regulatory or physiological limits,
and push the rates of reactions forward [3]. We cannot rule out, therefore, that pushing levels of
folate and SAMe methyl donors might increase DNA methylation beyond healthy levels.
According to Smith (2015), “It is now known that if there is too little methylation present, a gene
that causes disease may be expressed. Conversely, with too much methylation, a gene that
inhibits disease might be aberrantly suppressed.” If this is indeed true, we can assume there is
absolutely potential for harm. Once again, let’s explore what the literature says about excessive
DNA methylation and disease, specifically cancer, autoimmune conditions, immune
hypersensitivity and Downs Syndrome:
CANCER
Aberrant DNA methylation has been put forward as a possible contributing cause to cancers [6],
[43]. In cancer cell lines, both loci-specific DNA hyper- and hypo-methylation has been shown
to occur, indicating that both states can be characteristic of tumorigenesis [68]. Global DNA
hypermethylation is also apparent in various cancer cell lines, as shown in Figure 2.
The association between folic acid supplement use and colorectal cancer is one of the most
studied folic acid-cancer correlations, and we should note that a recent systematic review and
meta-analysis found inconsistent and inconclusive evidence for the effects of folic acid on
colorectal cancer risk [69]. However, looking at broad associations may miss important details
about the type, dose and effect of supplementation, and the folate, methylation and disease
status of the individual, some of which we can glean from individual studies. For example,
specific DNA site methylation in patients with stage II and III colon cancer has been
significantly associated with increased risk of disease recurrence as well as being an
independent predictor of poor overall survival (hazard ratio 2.9, 95% CI 1.5-5.8, P=0.002) and
disease-free survival (hazard ratio 4.0, 95% CI 1.6-10.2, P=0.003) [52]. In another study, a
randomized, controlled trial investigating the potential benefits of folic acid supplementation (1
mg/d) for the prevention of colorectal adenomas, researchers found that not only did folic acid
fail to reduce recurrence risk, but that the risks for recurrent colorectal adenoma and
noncolorectal cancers, especially prostate cancer, actually increased [70].
The influence of folic acid intake on breast cancer has also been explored and is considered
controversial. For example, in one observational study, dietary supplementation with folic acid

Figure 2: Methylation activity in various tissues [68]

The pooled cancer cell lines included in this figure were derived from breast, prostate, lung, ovarian,
endometrial, liver and pancreatic cancer cells, as well as neuroblastoma and leukemias.
greater or equal to 400 mcg/d was associated with a 20% increase in breast cancer risk compared
with those reporting no supplement intake [71]. In contrast, food-sourced folate has a protective
effect on cancer risk according to a 2014 Cochrane systematic review [72], and a recently
published retrospective analysis of data from 367,993 women indicated that higher food folate
intake is associated with a lower risk of sex-hormone receptor-negative breast cancer in
premenopausal women [73].
The connection between folate status and cancer has also been investigated. In an investigation
of women with breast cancer (n=204) compared with controls (n=408), individuals with the
highest tertile of plasma folate (median 17 nmol/L) had the highest likelihood of ERβ(-) breast
cancer (odds ratio 2.67, CI 1.44–4.92, P=0.001) [74]. Some of the same authors had previously
found an increased risk in breast cancer specifically when the MTHFR C667T polymorphism
was combined with high plasma folate levels [75], which may be concerning since patients who
know they have this polymorphism are among the most likely to take supplemental folates.

In another case-control study of over 300 individuals, it appeared that high levels of serum
folate acted as a promoter of the progression of existing benign tumors (polyps) to colorectal
cancer, but also as an inhibitor of carcinogenesis in healthy controls [76], leading researchers to
proposed that serum folate can actually have dual roles in the onset and progression of cancer.
In addition, recent cell studies point to potential dysregulation of one-carbon metabolism in
cancer cells, specifically methionine uptake transporters have been found to be overexpressed,
and the serine-glycine biosynthesis pathway is enhanced [77]. These offer perhaps some
explanation for the potentially harmful effect of folic acid or even other forms of folate where
there is a prior history of cancer.
We can’t know from these studies what folate derivative (see Figure 1) plays the biggest role in
these observed findings, since serum folate measures various folate vitamers, but we do know
that serum folate is largely made up of 5-MTHF (86.7%), with UMFA typically making up a
much smaller amount (4.0%) [7]. Whether the potency of the smaller amount of UMFA is
enough to cause the progression of pre-cancerous lesions, or whether high levels of 5-MTHF are
also implicated, is not possible to discern; leaving the practitioner having to make a clinical
judgment about what intervention to choose which will present least risk to the patient.
AUTOIMMUNITY
Systemic sclerosis is a poorly-understood autoimmune condition, characterized by endothelial
injury, immune abnormalities and fibrosis. It is increasingly thought to originate from
epigenetic dysfunction in immune cells that influence immune cell activation and proliferation
[78]. Alterations in various epigenetic mechanisms are implicated in the pathogenesis of the
disease. Hypermethylation of certain genes, Fli-1, KLF5 and BMPRII, reduce their anti-fibrotic
effects. Conversely, the overexpression of immune cells CD40L, CD70 and CD11a is also
involved, and is associated with hypomethylation of their corresponding genes.
The pathogenesis of other autoimmune conditions may also be influenced via methylation.
IgG4-related autoimmune pancreatitis (AIP) and other autoimmune-like phenotypes are
associated with MST1 (a serine/threonine kinase) deficiency in humans, which leads to T-cell
immunodeficiency and hypergammaglobulinemia with autoantibody production. IgG4-related
AIP patients who also exhibit extrapancreatic lesions demonstrate a significant increase in the
frequency of methylation of MST1 and reduced protein productions, suggesting that this gene is
regulated, at least in part, via methylation [79] and may contribute to the underlying disease
onset and progression. Aberrant methylation patterns, both hypo- and hyper have also been
observed in rheumatoid arthritis and autoimmune thyroid diseases. [80].
ALLERGY
In revisiting immune dysfunction we also find that researchers have hypothesized that
environmental exposures that increased DNA methylation may also increase the risk for allergic

disease by suppressing Th1 and T regulatory cell differentiation that would otherwise inhibit
the differentiation of allergy-promoting Th2 cells [60]. In a study of elderly men (n=704), minor
increases (0.31%) in methylation at gene Alu repeat sequences have been significantly
associated with incidence of prior sensitization to at least one allergen, raising the possibility
that even small changes in epigenetic regulators might have significant clinical effects [60]. Even
more compellingly, general hypermethylation at specific CpG sites has been proposed to be
useful for differentiating clinically non-reactive versus clinically reactive food-allergic
phenotypes, in a manner that appears to be even more predictive than serum IgE and skin prick
testing [81].
DOWNS SYNDROME
In Downs Syndrome, early-life downregulation of the TET family genes involved in DNA
demethylation, and downregulation of REST transcription factor expression and subsequent
methylation of REST-vacant sites, have been proposed as potential pathways leading to the
global DNA hypermethylation associated with the condition (Figure 3) [82].
Figure 3: Epigenetic mechanisms in the development of Down Syndrome (DS) phenotypes, adapted from
[83]

5.5 REASON TO TREAD CAREFULLY

While the effects of methylated folate or folic acid cannot be conclusively determined from the
studies and reviews discussed above, what is overwhelmingly apparent is that there are enough
unknowns to justify concern. Research is ongoing and it is not yet clear how aggressive 5-
MTHF, or other methylation supplementation, affects health or the process of disease. At the
very least these data suggest that we proceed with caution and focus on supporting the body’s
own healthy mechanisms for methylation balance rather than attempting to override them.
The reality is that metabolic and DNA methylation are incredibly complex, the latter both in its
own regulation and its regulation of gene expression with the added dimension of tissue-, site-,
and gene-specific nuances. Epigenomic regulation is also intricately dependent on many
environmental inputs, including both nutrients and lifestyle factors, which together make up
the detailed mosaic of methylation activity regulation.
A safer way to support methylation activity, especially over the longer term, may be through
food-based nutrients that provide the substrates and cofactors necessary for methylation
pathways, as well as food and lifestyle practices that have been shown to promote favorable
methylation activity and epigenetic imprints.

6 ASSESSMENT OF METHYLATION STATUS

While there are various assessments that can be used clinically to evaluate methylation status,
there is no single assessment tool that accurately reflects the complexity of methylation activity
in the body. Current laboratory assessments can provide insight into methylation-related
genetic polymorphisms, nutrient status, methylation-related neurotransmitters and
neurotransmitter metabolites, amino acids, hormones and metabolites, oxidative stress and
detoxification load, all of which can provide inputs into the picture of methylation status in any
one individual. Some measures, such as DNA methylation status, are not yet available to
practitioners and are generally limited to research studies. As DNA methylation assessment
does become available, care will be required on interpretation of data, as conflicting outcome
has been demonstrated in research based on different methodologies employed and tissue
methylation sites investigated. Furthermore, while technologies and research are rapidly
advancing, patterns of DNA methylation in humans across tissues, age, populations, disease or
environmental conditions (including dietary influence) are only just being characterized [84].
It is important that we not overemphasize any one single indicator, and be mindful of the
limitations of our interpretation as well as confounding factors. Plasma homocysteine, for
instance, can decrease as methylation activity improves, however it can also decrease when
oxidative stress levels are high, independently of methylation improvements. And as we’ve
discussed, only a few SNPs have known, quantifiable changes in enzymatic function, and even
then the overall effect on methylation is unknown. The practitioner must therefore rely on
multiple laboratory indicators in the context of clinical presentation to build an overall picture
of methylation health.
In this section we review methylation assessment options available to practitioners. A summary
checklist of these can be found in Appendix A.
6.1 GENETIC PROFILING

Genetic profiling can provide some indication of potential methylation status and disease risks.
Some gene SNPs lean towards heightened methylation activity (e.g. CBS), and others may
increase a tendency towards reduced methylation activity (e.g. MTHFR, BNMT, MTR, MTRR,
AHCY). However, the interpretation of overall effects of gene SNPs is complicated by other
polymorphisms and environmental inputs.
For example, it is known that the MTHFR C677T polymorphism is associated with an increased
risk of autism spectrum disorder (odds ratio = 1.42, 95% CI 1.09-1.85), but that this risk can be
mitigated by sufficient periconceptional folate or folic acid intake [85]. But if a maternal MTHFR
C677T polymorphism is combined with a CBS polymorphism, a lack of prenatal

supplementation with B vitamins and a fetal COMT polymorphism, the odds ratio for autism
spectrum disorder rises dramatically to 7.2 (CI = 2.3–22.4; P=0.05) [86].
This kind of clarity of disease risk related to genotype is unfortunately rare, since research into
the combined effects of gene SNPs is still very much in its infancy. In many situations the
practitioner will need to use careful clinical judgment to guide their interventions.
The methylation-related genes presented in Table 1 are frequently evaluated for SNPs.
Table 1: Genes related to methylation metabolism. Note that many SNPs do not result in clinically
significant changes to enzymatic function. However, understanding the biochemical role of the enzyme
coded for by the mutated gene can provide insight into biomarkers to test for and supportive interventions
to consider.
Gene Acronym Gene Full Name Enzyme & Role Possible SNP Effects
AHCY Adenosyl Encodes for the enzyme S- Reduced enzyme activity.

homocysteinase adenosyl homocysteine
Hypermethioninemia, s-
hydrolase (SAHH), which
adenosylhomocysteinema and
converts S-adenosyl
impaired methyltransferase
homocysteine (SAH, the
activity.
metabolic product of SAMe
methylation reactions) to
homocysteine. SAH is potently
inhibitory to methyltransferases.
BHMT Betaine-homocysteine Catalyzes an alternative route for Reduced enzyme activity.

methyltransferase the conversion of homocysteine
Reduced conversion of
to methionine in the liver.
homocysteine to methionine.
Theoretically associated with
hyperhomocysteinemia.
CBS Cystathionine-β- Converts homocysteine to Activity may be increased or

synthase cystathionine via transulfuration. decreased, depending on
This is an alternative pathway to mutation. Downstream
methionine resynthesis and the products potentially impacted
only route for homocysteine include sulfate, taurine,
elimination. glutathione and ammonia.
Upstream compounds
possibly impacted include
homocysteine and
homocystine.

CBS is overexpressed in
patients with Down Syndrome
resulting in
hypohomocysteinemia.
COMT Catechol-O- COMT enzymes metabolize the The most studied COMT SNP
methyltransferase catecholamine neurotransmitters is Val158Met, associated with
dopamine, norepinephrine and up to a 35-50% reduced
epinephrine, as well as the activity as compared to wild
catecholestrogens (produced type COMT [87].
from estradiol).
Reduced clearance of
Note that there are two different catacholamines: dopamine,
forms of the COMT enzyme, epinephrine, norepinephrine).
soluble (associated with estrogen Accumulation of
metabolism in the liver, kidneys catecholestrogens.
and GI tract) and membrane
bound (associated with brain
neurotransmitter metabolism).
MAO-A Monoamine oxidase MAO-A is primarily involved in MAO-A and MAO-B

enzymes A and B the catabolism of serotonin, mutations may be associated
MAO-B
norepinephrine and dopamine. with reduced clearance of
MAO-B primariy catabolizes dopamine, serotonin,
dopamine, phenylethylamine epinephrine, norepinephrine,
(PEA), and N-Methylhistamine. N-Methylhistamine and trace
Both MAO-A and B catabolize amines [88].
trace amines including
tryptamine and tyramine.
MAT1A Methionine Encodes for MAT which forms Results in reduced enzyme
adenosyltransferase I, SAMe from methionine. activity.
alpha
Alcohol inactivates liver MAT May result in decreased SAMe
[89]. and compromised methylation
activity; increased
homocysteine

MTHFR Methylenetetrahydro- Converts 5,10-methylene THF May cause reduced enzyme

folate reductase irreversibly to 5-methyl THF activity.
which is the active form used in
Most studied SNPs are C677T
the conversion of homocysteine
and A1298C.
to methionine for subsequent
SAMe formation. May result in low SAMe,
elevated homocysteine and
reduced methyltransferase
activity.
MTR 5-methyl- Encodes for the enzyme May result in reduced enzyme
tetrahydrofolate- methionine synthase (MS) which activity
homocysteine catalyzes the final step in
Low THF, increased
methyltransferase methionine biosynthesis. MS
homocysteine, decreased
converts homocysteine to
SAMe, increased reactive
methionine by transferring a
oxygen species.
methyl group from
methylcobalamin to
homocysteine to form
methionine. The methyl group is
obtained from 5-mTHF,
transforming it into THF.
MTRR 5-methyl- Encodes for the enzyme Decreased methionine

tetrahydrofolate- methionine synthase reductase synthase activity, increased
homocysteine which re-methylates cobalamin homocysteine and reactive
methyltransferase using 5-mTHF for use by oxygen species, decreased
reductase methionine synthase. SAMe.
Source: adapted from [6], [22]

6.2 NUTRIENT STATUS

Folate and vitamin B12 are perhaps the most well-known nutrients that play a direct role in
methylation activity, however there are multiple other nutrients involved with methylation
enzymes and pathways, either as substrates or cofactors (Figure 4).
Figure 4: Nutrients that support methylation pathways
There are various methods for the assessment of nutrient status (Table 2), including laboratory
analytes and physical exam findings. Dietary intake assessment, via analysis of diet diaries, also
provides a view of nutrient intake and can be a useful tool for evaluating nutrient inputs and as
a basis for adjustment of nutrient intake. In our practice we routinely use nutrient intake
analyses in conjunction with laboratory and physical functional status assessments.

Table 2: Roles and assessment of nutrients involved in methylation activity.

Laboratory tests are listed in order of preferred specimen. Note that physical exam findings are generally
not specific and confirmatory testing is recommended, especially with regard to identifying causes of
cardiac arrhythmias.
Nutrient Role Assessment
Methionine Precursor to SAMe Plasma
Cysteine Spares homocysteine to enter the Plasma

methylation pathway and can act as a
precursor for methionine and SAMe
Taurine Spares homocysteine to enter the Plasma

methylation pathway to create SAMe
DHA Upregulates MTHFR expression, RBC or plasma

downregulates MAT expression,
Physical exam: xeroderma,
reduces homocysteine [90]
dermatitis, keratosis pilaris, sensory
neuropathy, poor wound healing
Zinc Cofactor for betaine-homocysteine S- RBC, plasma, hair

methyltransferase (BHMT) which
Physical exam: loss of taste/smell,
converts homocysteine to methionine
delayed wound healing, oral
candidiasis, nail changes include
leukonychia, koilonychia, Beau’s
lines, onychorrhexis
Magnesium Cofactor for conversion of RBC, whole blood, plasma, serum,

methionine to SAMe. Magnesium is urine. Magnesium deficiency can
required for any ATP and/or B6 cause refractory hypernatremia,
dependent enzyme hypokalemia and hypocalcemia
Physical exam: muscle spasms

including blepharospasm, tremor,
cardiac arrhythmias. Nail changes
include onychorrhexis.

Severe deficiency: tetany, loss of

appetite, nausea, vomiting
Potassium Cofactor for MAT enzyme RBC, serum (obtain both for best
assessment)
Physical exam: muscle spasms

including blepharospasm and
tremors. Cardiac arrhythmia (confirm
with laboratory testing before
prescribing supplemental potassium).
Food sourced potassium is always
safe to prescribe in healthy
individuals not taking potassium
sparing medications)
Riboflavin (vitamin Cofactor for MTHFR and MTRR Urine alpha-keto acids, plasma
B2) enzymes.
Physical exam: angular chelitis,
cheilosis, glossitis, recurrent apthae,
poor mucocutaneous border; nail
changes caused by general B vitamin
deficiency include beading,
onychorrexis, koilonychia
Niacin (vitamin B3) Cofactor for MTHFR and MTRR Serum, urine lactate & pyruvate,
enzymes alpha keto acids, picolinate

cheilosis, glossitis, stomatitis, poor
mucocutaneous border; nail changes
caused by general B vitamin
Pyridoxine (vitamin Required for formation of 5,10- Urine xanthurenate

B6) methylene THF, the form of folate
Urine kynurenate
that is the substrate for MTHFR.
Cofactor for cystathionine beta Plasma homocysteine
synthase (CBS) Plasma B6

cheilosis, burning mouth syndrome,

Note that B6-dependent enzymes glossitis, lip fissures, oral sensitivity,

always requires magnesium poor mucocutaneous border; nail
Folate Source of folate derivatives for Urine formininoglutamate

MTHFR and methionine synthesis
Plasma homocysteine
RBC folate*
Macrocytosis/macrocytic anemia
(with B12)
Whole blood neutrophil

hypersegmentation
Serum folate

cheilosis, candidiasis, glossitis,
recurrent apthae, stomatitis,
periodontal disease; sensory
neuropathy. Nail changes caused by
general B vitamin deficiency include
beading, onychorrexis, koilonychia
Vitamin B12 Cofactor for MTR as Urine or serum methylmalonate

methylcobalamin. B12 is
Plasma homocysteine
remethylated via MTRR (5-mTFH
provides the methyl group) Serum vitamin B12
Macrocytosis/macrocytic anemia
(with folate)
Physical exam: Angular chelitis,

cheilosis, glossitis, macroglossia,
recurrent apthae, stomatitis,
periodontal disease, sensory
neuropathy, hyperpigmentation,
vitiligo, atopic dermatitis. Nail


Betaine Cofactor for BHMT; activator for CBS Not typically measured
(trimethylglycine) enzyme
Choline Can convert to betaine in the body. Plasma

Spares tetrahydrofolate.
Sulfur Spares homocysteine for conversion Sulfur-containing amino acids in

to SAMe, especially in presence of amino acid profiles: methionine,
oxidative stress (see below) cysteine/cystine,
homocysteine/homocystine,
cystathionine, taurine.
Urine sulfate
Physical exam: Sulfur deficiency can

result in broad changes to keratin-
rich tissues, including nails, skin and
hair

* The CDC has identified an optimal red blood cell folate range (>906 nmol/L) for the prevention of
neural tube defects [91].
6.3 METHYLATION METABOLITES

A number of additional laboratory-assessed metabolites are also used in the assessment of
methylation status (Table 3).
Table 3: Additional metabolites used in the assessment of methylation status
Metabolite Significance Assessment
Homocysteine Elevated homocysteine can indicate Plasma

low formation of SAMe for
methylation reactions

SAMe Low SAMe can indicate deficiency of Plasma

methyl donors for methylation
reactions
SAH Elevated SAH can indicate poor Plasma

conversion of homocysteine to
methionine and inhibition of DNA
methylation
SAMe:SAH ratio Considered a ‘methylation index’, a -

low ratio is often interpreted as an
indicator of poor methylation status.
Other factors may also lower this
ratio, however, such as increased
oxidative stress
Cystathionine High cystathionine can indicate early- Plasma

stage elevated oxidative stress which
can inform the interpretation of
homocysteine results
Additional methylation-related substrates, amino acids and amino acid derivative

compounds may also be suggestive of methylation status. Care is advised in interpretation.
These include:
• Compounds that interact with the folate cycle: glycine, serine, threonine, sarcosine,
phosphoserine, ethanolomine, phosphoethanolamine. phenylalanine, tyrosine,
tetrahydrobiopterin (BH4) products neopterin/biopterin.
• Compounds produced via SAMe-dependent methyltransferases: vanilmandilate
(metabolite of epinephrine and norepinephrine), homovanillate (metabolite of
dopamine), melatonin and creatinine.
• Substrates metabolized via SAMe methylation: histamine, estrogens.
Resources for laboratory interpretation:
• Lord & Bralley, 2012, Laboratory Evaluations for Integrative and Functional
Medicine [22].
• Metametrix Handbook (downloadable from Genova.net).
• Laboratories offering evaluation panels often have interpretive guides and training
options.

6.4 NUTRIENT ASSIMILATION CAPABILITY

Nutrient status is dependent on various factors. While optimal nutrient status starts with food
ingestion, there is a process of digestion, absorption, transport, utilization and metabolism of
each nutrient that must work in concert to deliver the required effect. Two of the most common
and addressable issues in that chain are digestion and absorption.
To that end, practitioners using a MDL program may also evaluate and correct gastric function,
pancreatic function, intestinal dysbiosis, intestinal permeability, food sensitivities, and
malabsorption issues, all of which can have an impact on the absorption of nutrients necessary
for methylation function.
6.5 INFLAMMATION
Inflammation, and its associated increase in cytokine production, can interfere with methylation
various ways. DNA methylation is affected by inflammation-related signaling molecules.
Cytokines, chemokines, free radicals, prostaglandins, growth factors and matrix
metalloproteinases are among the molecules produced during inflammation, and these induce
epigenetic changes including DNA methylation [92]. IL-1β for example, suppresses p53
expression [93], creating a more favorable environment for tumorigenesis. NFκB, a central
transcription factor activated by inflammation, regulates the expression of more than 400 genes.
It is also a direct regulator of NKκB-dependent histone demethylase which in turn regulates the
fate and transdifferentiation of tumor cells [93]. IL-6, another potent inflammatory signaling
molecule, regulates the activity of DNMTs, microRNAs and histone methyltransferases, and is
able to alter the epigenetics of p53 tumor suppressor genes in a way that reduces their
expression [93], [94]. TNF-alpha induces increases in mitotically-preserved and region-specific
DNA methylation in a manner that appears to associate with impaired cellular differentiation
and renewal [95].
In vitro evidence suggests that inflammation may also drive the production of methyl radicals
which induce DNA methylation of the normally unmethylated tumor suppressor genes, leading
to gene silencing and carcinogenesis [96].
Inflammation can also contribute to a metabolic milieu that drains methylation resources, for
instance via dysregulation of glucose homeostasis. Pro-inflammatory molecules interfere with
insulin signaling in peripheral tissues [97] and reducing inflammatory mediators improves
insulin signaling [98]. Insulin dysfunction and hyperglycemia promote increased oxidative
stress which drives increased utilization of glutathione and depleted homocysteine, methionine
and SAMe. Further, disordered DNA methylation patterns influencing metabolism and
inflammation were identified in adipose tissue from subjects with type 2 diabetes [99].

Table 4: Factors in the assessment of excess inflammation
Category Inflammatory Factor Significance
Anthropometrics Weight Overweight and obesity,

especially excess
Body-mass index
abdominal adipose tissue,
Waist circumference is associated with
increased levels of
inflammation
Standard CRP Laboratory markers that

laboratory are routinely used in the
Ferritin
inflammation assessment of
indicators Erythrocyte Sedimentation inflammatory status
Rate
Microbial Dysbiosis Disturbances in bacterial

assessment populations residing in the
Small intestine bacterial
gastrointestinal tract can
overgrowth (SIBO)
generate pro-inflammatory
Periodontitis compounds that can enter
circulation
Comorbidity Various, e.g. active Active autoimmunity or

autoimmunity, co-infection infection can increase
systemic inflammation
6.6 OXIDATIVE STRESS

Oxidative stress is closely related to inflammation. States of high, or chronic, oxidative stress
can negatively impact methylation metabolism via two mechanisms. Firstly, oxidative stress
increases the demand for glutathione synthesis, which pulls homocysteine towards
transulfuration pathways, at the expense of methylation pathways and SAMe formation [39].
Secondly, oxidative stress and increased hydroxyl radical formation can damage DNA and
impair the ability of DNA methyltransferase enzymes to appropriately methylate DNA; this can
lead to global DNA hypomethylation and specific areas of hypermethylation [4].
DNA guanine nucleotides can be major sites of DNA oxidative damage, and are frequently
used as a biomarker of DNA-level oxidative stress (8OHdG). Normally, guanine acts as a

hydrogen bond acceptor in the formation of methyl binding protein (MBP)-DNA complexes.
However, oxidation of guanine significantly diminishes MBP binding when adjacent to the 5-
methyl cytosine nucleotide. In addition, 5-methylcytosine (5-mC) is also susceptible to oxidation
(hydroxylation), forming 5-hydroxymethylcytosine (5-hmC), in the presence of environmental
stimuli such as oxidative stress. This can interfere with DNA-protein interaction and inhibits the
binding affinity to MBPs, leading to potentially heritable epigenetic alterations. [4]
Most-commonly used methods to detect DNA methylation do not differentiate between 5-mC
and 5-hmC, which may prove to be an important distinction, especially in the brain where most
DNA hydroxymethylation appears to present [100]. There is evidence that acute psychological
stress can increase DNA hydroxymethylation in the hippocampal glucocorticoid receptor gene
and that this epigenetic change predisposes to neuropsychiatric and neurodegenerative
disorders [100]. Aging is also associated with increases in 5-hmC in the brain, and may be
prevented by caloric restriction and antioxidant upregulation [101].
Table 5: Common analytes in the assessment of oxidative stress
Analyte Significance
8-OHdG A marker for DNA damage induced by

oxidative stress
Alpha- A marker for glutathione status

hydroxybutyrate
Pyroglutamate (5- A marker for glutathione loss and decreased

oxoproline) antioxidant capacity
F2-isoprostanes Product of free radical activity on arachidonic

acid
Lipid peroxides Product of free radical activity on lipids
Source: [22]

7 THE METHYLATION DIET AND LIFESTYLE

We prescribe the full MDL or portions of the program to all of our patients. We are pleased to report that
thus far our patients have responded well, both in terms of palatability and “do-ability” of the diet as well
as clinically. For example: a 57-year-old male presenting with diffuse myalgia and arthralgia and a
history of toxic mold exposure, who complained of years-long methyl donor intolerance, had a baseline
homocysteine of 15.7. After one month of the MDL program, his follow-up homocysteine is 11.8, which
appears associated with a modest reduction in pain. No other changes to his plan were made.
Functional medicine practitioners may utilize The MDL program in various ways:
• As a stand-alone intervention for long-term support
• Alongside folate and other nutrient supplementation to support effectiveness
• As an alternative intervention for individuals who do not tolerate methyl donor
supplementation
In this section, we review the foundational interventions that are relevant to the MDL program.
Readers may also find a summary checklist of these interventions in Appendix B.

7.1 FOOD-BASED NUTRIENTS

Recommendation: As possible, use nutrients from foods for methylation support and for addressing
significant genetic SNPs
It is reasonable to conclude that supporting methylation status through non-fortified whole

foods is a lower-risk and effective intervention, as long as adequate status of the relevant
nutrients can be maintained.
When compared side-by-side in a 16-week human placebo-controlled trial, an increase of 200

mcg/d folate from folate-rich foods (from a baseline average of 292 mcg/d) showed the same
ability (no statistical significance between effects) to increase plasma and erythrocyte folate
levels, and lower homocysteine compared with an equal amount of supplemental folic acid or
5-mTHF (as Metafolin®) [102]. Dietary folate, along with other lifestyle factors, has also been
shown to have a significant, favorable effect on DNA methylation [4], [25]. There is no upper
limit set for folate intake sourced from non-fortified foods, and at this time of writing we know
of no studies showing adverse effects from sourcing folates and other methylation nutrients
from foods.
The question of what level of nutrient intake is sufficient to optimize methylation status has no
definitive answer, and will inevitably vary from individual to individual based on their genetic
fingerprint and environmental factors. A Cochrane systematic review, published in 2014, found
that food-sourced folate had a protective effect on cancer risk (specifically breast cancer) within
the range of 153 – 400 mcg/d [72], suggesting that high dosing is not necessarily advantageous
for the general population. However, it may be reasonable to assume that certain populations,
often those whose health concerns lead them to seek out Functional Medicine, may have genetic
or environmental disturbances that merit higher nutrient intakes.
There are various nutrients involved with methylation enzymes and pathways, either as
substrates or cofactors, as shown in Figure 4. Table 6 lists out these nutrients of particular
interest and their dietary sources. Some of these nutrients are already used as targeted
supplements by many functional medicine practitioners, and are a central component of the
MDL Food Plan and Menu Plans.

Table 6: Methylation nutrients and their dietary sources
Nutrient Rich Dietary Sources (Sourced from [103] unless otherwise

noted)
Methionine Egg, cod, whitefish, sesame seeds, spirulina, parmesan cheese,

sunflower seeds, Brazil nuts, chicken, beef, lamb, salmon,
buffalo, turkey, halibut, pork, anchovy, Romano cheese, game
meats, gruyere cheese, goat cheese, goose, duck, snapper,
tilapia, mackerel, haddock, lobster, pumpkin seeds, sardine,
herring, bison, game meats.
Cysteine Egg, sesame, sunflower, beef (especially liver), cod, tofu,

spirulina, soybeans, pork, whitefish, fish roe, butternuts, black
walnuts, sunflower seeds, goose, duck, watermelon seeds,
buffalo, lamb, chicken, oats, pumpkin seeds, quail, octopus,
halibut, pistachio nuts, flaxseed, clams.
Taurine Animal and fish protein, eggs and brewer’s yeast.
DHA Fish oil, cod liver oil, mackerel, salmon, fish roe, anchovy,
whitefish, herring, trout, bass, tilefish, sardine, halibut,
22:6(n-3)
oysters, squid, flatfish, mussels, shrimp, crab, perch, scallops.
Zinc Oysters, pumpkin seeds, sesame seeds, chervil, beef, game

meats, lamb, poppy seed, shiitake mushroom, cardamom,
celery seed, crab, bison, turkey, pork, peanuts, pine nuts,
cocoa, thyme, parsley, rice bran, basil, agar seaweed, cashews,
lobster, mustard seed, dark rye.
Magnesium Seaweed (agar), herbs, spices, bran, pumpkin seeds, cocoa,

flaxseed, Brazil nuts, sunflower seeds, sesame seeds, poppy
seeds, almonds, cashews, buckwheat, amaranth, rye,
molasses, walnuts, quinoa, great northern beans, mung beans,
teff, tofu, chickpeas, oats, daikon radish, bulgur,
lambsquarters, hazelnuts, leeks, black beans, kidney beans,
horseradish.
Potassium Dried herbs, daikon radishes, sun-dried tomatoes, turmeric,

cocoa, chili powder, dried apricots, lima beans, oregano, white
beans, shiitake mushrooms, kidney beans, pinto beans, great
norther beans, lambsquarters, adzuki beans, mung beans,
pistachio nuts, lentils, pumpkin seeds, sunflower seeds, yam,

flaxseeds, peanuts, hazelnuts, cashew nuts, wild salmon,

clam, pine nuts, tahini, potatoes, coconut meal, Swiss chard,
portabella mushrooms, pork, cod, avocado, spinach.
Riboflavin (vitamin Lamb liver, spirulina, beef liver, egg, paprika, chives,
B2) coriander leaf (cilantro), spearmint, chicken liver, tarragon,
shiitake mushrooms, parsley, almonds, fish roe, cayenne
pepper, duck liver, goose liver, chili powder, soybeans, game
meat, daikon radish, chervil, goat cheese, mackerel, brie
cheese, sesame.
Niacin (vitamin B3) Anchovy, beef liver, lamb liver, peanuts, chicken, chicken
liver, shiitake mushrooms, sesame seeds, salmon, spirulina,
pork, cilantro (coriander leaf), mackerel, parsley, beef, game
meats, sun-dried tomatoes, tarragon, trout, lamb, chili
powder, mustard seed, duck, cod, sunflower seeds.
Pyridoxine Rice bran, paprika, chili powder, ancho peppers, sage,

cayenne pepper, tarragon, basil, chives, turmeric, bay leaf,
rosemary, dill, pistachio nuts, baker’s yeast, turkey liver,
parsley, sunflower seeds, garlic, oregano, leeks, marjoram,
curry powder, shiitake mushrooms, salmon, chervil, celery
seed, chicken liver, cod, ginger, sesame seeds, palm heart,
sunflower seeds, prunes, pork, brown rice, beef, game meats,
molasses, chestnuts, octopus, goose, cornmeal, trout, daikon
radishes, potatoes, cilantro (coriander leaf), fenugreek seed,
amaranth, cloves, hazelnuts, black walnuts, soybean, thyme,
lentils, peanuts, English walnuts, chickpeas (garbanzo beans),
dried apricots.
Folate Liver (duck, goose, turkey, chicken, beef), mung beans,

chickpeas (garbanzo beans), spearmint, pinto beans, great
northern beans, lentils, black beans, fava beans, kidney beans,
soybeans, leeks, navy beans, rosemary, daikon radishes, split
peas, basil, cilantro (coriander leaf), marjoram, oregano, sage,
tarragon, thyme, peanuts, sunflower seeds, wakame seaweed,
spinach, turnip greens, asparagus, mustard greens, quinoa,
kelp seaweed, bay leaf, parsley, pinto beans, black eye peas,
collard greens, shiitake mushrooms, parsley, dill, okra, egg,
peanuts, artichokes.

Vitamin B12 Clams, liver (lamb, beef, turkey, duck, goose, chicken),
oysters, mussels, mackerel, whitefish, salmon, crab, cod,
herring, trout, game meat, eggs, beef, chicken, goose, pork,
lamb, snapper, lobster.
Betaine Beets, lambsquarters, spinach, and quinoa. Liver, sunflower

(trimethylglycine) seeds, kamut, and rye are also good sources. [104]
Choline Egg yolk and liver are excellent sources. Choline is also found
in meats, especially beef, salmon, whitefish, trout, soybeans,
lentils, cauliflower and flaxseeds [104], [105].
Sulfur Egg, cabbage, Brussels sprouts, leeks, horseradish, ginger,

mustard, fish, shellfish, lamb, beef, chicken, pork, duck, goose,
turkey, lentils, peas, butter beans, barley, oatmeal, cress,
haricot beans, Brazil nuts, almonds, peanuts, walnuts [106].

Depending on the genotype of the individual, nutrient needs can be further customized to
support potential enzyme deficiencies. Individuals with specific SNPs may benefit from
increased intake of cofactor nutrients utilized by the associated enzyme since it has been shown
that high cofactor intake can push the rate of enzymatic reactions forward [3]. Table 7 lists
frequently evaluated methylation-related genes and the nutrients that can be utilized to support
activity.
Table 7: Methylation-related genes and nutrition to support SNPs
Gene Cofactor Nutrient Support
MTHFR Riboflavin, niacin
MTR Vitamin B12, zinc
MTRR Riboflavin, B12
MAT1A Magnesium, potassium*
MAO Riboflavin, iron
COMT Magnesium
CBS Vitamin B6, magnesium betaine
MTRR Vitamin B12
BHMT Betaine, choline

*While there are no known risks of dietary potassium intake, potassium supplementation should
be physician supervised.
7.2 SUPPORT FOR NUTRIENT ASSIMILATION

Recommendation: Support optimal micronutrient assimilation with the Five-R gut repair protocol
Where a need is indicated, either by laboratory testing or physical exam findings, the Five-R
Protocol, outlined in Table 8, is an ideal way to improve nutrient assimilation and functional
status. It can be done either alongside a short-term course of methylation supplementation
(with subsequent transition to the MDL) or alongside the MDL from the start.

Table 8: Overview of the Five-R Protocol for Optimizing Gut Function
Step Target Explanation
Remove Microbial overgrowth or Herbal or pharmaceutical

pathogens, reactive or treatments to lower
destructive foods pathogenic load. Identify
and remove offending
foods (clean food sources,
Elimination Diet). Review
medications.
Replace Digestive capacity Support digestive function

through oral digestive
enzymes, acid, bile or
factors that promote
digestive secretions (e.g.
bitters, cholagogues).
Re-inoculate Microbiome health Probiotics and prebiotics to

favorably repopulate
bacterial populations.
Repair Mucosal lining and Targeted supplementation

immune integrity for mucosal and immune
health.
Rebalance Lifestyle Stress reduction and stress

management, sleep
hygiene, exercise.
7.3 MICROBIOME
Recommendation: Support balanced microbial populations and folate-producing species
Early research findings suggest that the microbiome may play a role in regulating host DNA
methylation activity, at least in their local environment. DNA methylation of intestinal
epithelial cells is shown to be significantly dysregulated and reduced in germ-free mouse
models when compared with conventional controls [107]. This study also showed that
reestablishing commensal bacterial populations via fecal transplant correlates with significant

increases in CpG methylation. Gut microbes also produce butyrate, which potently inhibits
histone deacetylase and also appears to affect DNA methylation [108], [109]. Researchers argue
that these findings suggest a sophisticated, directive role for microbes in host epigenetic
regulation, beyond simple facilitation [107].
Specific bacterial species may also exert different effects on DNA methylation. In one human
pilot study, higher levels of the bacterial phylum Firmicutes (vs bacterial phylum Bacteroidetes)
was associated with increased promoter methylation of 568 genes, and decreased promoter
methylation of 245 genes (P=0.05). The genes affected were associated with cardiovascular
disease, inflammation, metabolic pathways and cancer [110]. Previous studies in humans have
identified various Firmicutes/Bacteroidetes ratios in obese individuals [111].
The gut microbiota also affects nutrient status, and in this role may also indirectly impair or
support methylation activity. Most Lactobacillus species are in vitro consumers of folate with the
exception of L. plantarum strains which can produce folate in the presence of para-aminobenzoic
acid (PABA). Many Bifidobacteria species, especially strains of B. bifidum and B. infantis, are folate
producers, along with B. breve, B. longum, B. adolescentis, and B. pseudocatenulatum [112]. Most of
these species also produce folate in both its THF and 5mTHF forms, with B. adolescentis
producing the highest levels of methylated folate [113]. In vivo, the administration of B.
adolescentis (MB 227 and MB 239) and B. pseudocatenulatum (MB 116) raised serum folate levels in
folate-deficient rats, and the co-administration of prebiotic fructans raised serum folate levels
further still [114]. While human folate absorption occurs primarily in the small intestine, it also
occurs in the colon [115]. Administration of B. longum to hemodialysis patients reduced serum
homocysteine in a manner attributed to the increased supply of folate produced by this species
in the gastrointestinal tract [116].
In addition, dysregulation of commensal populations or overgrowth of bacteria in the small
intestine can hinder general nutrient absorption and appetite signaling with consequences for
functional status of methylation substrates and cofactors [117]. And, as an example of the
interconnectivity between the various inputs to methylation health, unfavorable microbial
balance may underlie local and systemic inflammation [118], which, as we have reviewed, can
also have effects on methylation activity.
7.4 INFLAMMATION
Recommendation: Adopt an anti-inflammatory diet and lifestyle
Strategies to reduce inflammation are appropriate for methylation support (see Section 6.5.
While a full exploration of all anti-inflammatory interventions is beyond the scope of this book,
the following provide a summary of potential actions and are common approaches used in
Functional Medicine:

• Regulate blood glucose: chronically elevated circulating glucose levels, and also acute,
postprandial glucose spikes activate oxidative stress [119], indicating that both aspects of
glucose control should be addressed.
• Healthy weight maintenance: Adipose tissue produces pro-inflammatory cytokines
including TNF-alpha and IL-6 [120] and is associated with aberrant DNA methylation
patterns [99]. A higher body-mass index (BMI) and especially central adiposity is a
driver of chronic, systemic inflammation [121].
• Resolve microbially-driven inflammation: Excessive levels of bacteria or dysbiosis in the
GI tract promote higher levels of local and systemic inflammation [122]. Bacterial pro-
inflammatory compounds with systemic effects can derive from the small and large
intestine, and also in the stomach, and oral cavity. Pro-inflammatory pathogenic
bacterial species may also take up residence in internal tissues such as atherosclerotic
plaque [123]. Helicobacter pylori, a potential pathogen in the stomach, is also associated
with aberrant DNA methylation [124].
• Reduce exposure and sensitization to food antigens: food allergies and sensitivities have
been shown to increase inflammation via innate immune activation [125].
• Adopt an anti-inflammatory diet: which avoids pro-inflammatory foods such as sugars,
refined carbohydrates, conventionally-raised animal products, refined vegetable oils,
hydrogenated fats, and includes phytonutrient-rich whole plant foods and omega-3 fatty
acids.
• Support an anti-inflammatory lifestyle: Pro-inflammatory lifestyle factors such as stress
[126] and sedentary behavior [127] can be mitigated by stress management techniques
and physical activity. Lifestyle factors also exert effects on methylation activity that are
independent of their potential actions on inflammation.
7.5 OXIDATIVE STRESS

Recommendation: Reduce sources of oxidative stress and support balanced antioxidant capacity
Sources of oxidative stress can be metabolic, dietary or environmental: excessive calories,
excessive sugars/refined carbohydrates, too little or too much exercise, excessive alcohol
consumption, tobacco smoke, air pollutants, fungal toxins, charbroiled foods (and other
advanced glycation end products), ionizing radiation, chronic infections, poor sleep, and gut
dysbiosis can all contribute to oxidative stress. Addressing oxidative stress involves reducing
sources as well as support in the form of antioxidants as found in a high plant-food diet, herbs,
spices, nuts, seeds and unrefined oils. Specific supplements such as N-acetylcysteine, alpha
lipoic acid and coenzyme Q10 may also be useful where there is a specific need that cannot be
met via diet alone.

7.6 DETOXIFICATION
Recommendation: Reduce exposure to environmental toxins and support biotransformation and
elimination
Methylation is an important detoxification pathway, and so high exposure to environmental

toxins such as heavy metals and chemicals can place excessive demand on methyl donors and
limit their availability for other uses. Environmental toxins may also exert their effects on DNA
methylation via other mechanisms such as endocrine disruption, oxidative stress and
inflammation [128].
Figure 5: Potential Mechanisms Linking Environmental Toxin Exposure with Epigenetic Effects, adapted
from [128]

The following environmental toxins are among those that have been found to produce DNA
methylation alterations:
• Pesticides [2] • Benzene [33]
• Fertilizer [2] • Mold toxins (aflatoxin, fumonisin)
[132]
• Automobile fumes [2], [129]
• Arsenic [128], [133], [134]
• Bisphenol A [128], [130]
• Mercury [133], [134]
• Phthalates [130]
• Lead [134]
• Persistent Organic Pollutants (POPs)
[128], [131] • Cadmium [128], [134]
• Jet fuel [130] • Nickel [128]
Heavy metals may be particularly problematic. Specific DNMT inhibition and reduced DNMT
gene expression has been shown with lead exposure [134]. Cadmium appears to induce DNA
hypomethylation via DNMT inhibition in the short term, but may actually have the opposite
effect, that of hypermethylation, when chronic exposure is present [134]. In vitro research
suggests that one mechanism involved in aberrant DNA hypermethylation is via the induction
of toxin or inflammation- mediated methyl radicals (from oxidized methionine) that prompt the
direct formation of DNA hypermethylation of tumor suppressor genes resulting in gene
silencing and oncogenesis [96]. Oxidized methionine formation has been detected in smokers,
inflammation and aging [96]. Inorganic arsenic is detoxified in the body by methylation, leading
researchers to conclude that arsenic exposure may drain the endogenous pool of methyl donors
[134].
Total exposure to toxins such as persistent organic pollutants (POPs) and heavy metals may
have cumulative and long-lasting effects. Manikkam et al. (2012), investigating the DNA
methylation effects of bisphenol A, phthalates, digoxin and jet fuel (as listed above) also found
that the epigenetic alterations persisted across generations and appeared to induce early onset
puberty four generations later in rodents [130].
Environmental toxins may also inhibit healthy methylation activity by interfering with other
folate mechanisms. Fumonisins (a type of mold toxin), for example, have been found to inhibit
the proper function of folate binding proteins (human folate receptor alpha) [132].
In light of our growing understanding of how toxins influence methylation, and other health
aspects, reducing exposure where possible is essential. This may involve the assessment and
remediation of exposures to mold, lead, and mercury amalgams, for example, minimizing the
use of plastic food containers, avoiding high-mercury fish, and switching to nontoxic household

and personal care products. The Environmental Working Group (www.ewg.org) provides an
excellent resource for further understanding sources of toxin exposure, and independent
product testing.
Supporting endogenous biotransformation via Phase I and Phase II detoxification pathways, as
well as well-functioning elimination, is also essential. Short term use of supplement protocols
for detoxification are often used in functional medicine, where an excessive toxic burden is
indicated. Food and lifestyle also present an opportunity to support detoxification. The
following are basic principles to follow for everyday detoxification support:
• Proper hydration
• Adequate fiber sources
• Low-toxin foods including organic, and antibiotic and hormone-free
• High intake of colorful plant foods, especially deep greens and berries
• Regular intake of cruciferous vegetables
• Adequate protein intake
• Maintain micronutrient intake
7.7 STRESS MANAGEMENT

Recommendation: Manage stress exposure and response
States of high psychological and physiological stress increase the production of the
catecholamines epinephrine and norepinephrine, which require methylation for their
biosynthesis, metabolism and excretion. High methylation activity in these pathways draws on
the available pool of SAMe, and can lower the availability of this methyl donor for other
reactions. Stress reduction and management is, therefore, an appropriate intervention for
sparing methyl donors for other functions.
In addition to metabolic methylation, psychological stress can also alter DNA methylation via
mechanisms distinct from competitive demand for methyl donors. And it is clear that, once
again, there is a significant amount of complexity that governs the overall and site-specific
effect, and that our current understanding is limited. Methylation of the promoter region of
genes coding for the glucocorticoid receptor, a key modulator of the HPA axis and stress
response, has been shown to be differentially altered in various stress states including early life
stress, post-traumatic stress disorder, and chronic fatigue syndrome [135], [136].
PRENATAL AND EARLY LIFE STRESS EFFECTS

Stress sensitivity: We know that stress-mediated epigenetic ‘priming’ via methylation during
critical developmental windows is associated with later onset of psychopathology. For instance,
and as we reviewed earlier, low levels of maternal nurturing is associated with altered levels of
© 2016 Dr. K Fitzgerald, ND www.drkarafitzgerald.com 57

DNA methylation in the glucocorticoid receptor promoter, and increased expression of the
receptor, suggesting that traumatic experiences, perhaps especially during vulnerable periods
of development, might ‘prime’ an individual for a later, hyper-stress response [31]. Some
authors have theorized that methylation changes that potentiate the effects of the stress
response, may explain the connections between stress and diseases such as asthma [137].
Metabolic risk: Prenatal maternal stress, as evaluated after the January 1998 Quebec ice storm,
correlates with increased central adiposity and BMI in offspring at age 13 ½, and these changes
are thought to be, in part, mediated via DNA methylation [138].
STRESS EFFECTS OUTSIDE THE PRENATAL AND PERINATAL TIME PERIODS

Stress sensitivity: Traumatic childhood experiences, including maltreatment, and parental
death or desertion, outside of the prenatal and perinatal developmental periods also appear to
alter methylation of the glucocorticoid receptor gene promoter, corresponding with attenuated
cortisol responsiveness [139].
STRESS AND INFLAMMATION

Acute and chronic stress also directly increase circulating inflammatory factors including IL-1β,
CRP and IL-6, mediated via upregulation of the NLRP3 inflammasome [140], and this is may be
a significant way in which stress mediates epigenetic alterations. The effects of inflammation on
methylation activity are reviewed above.
7.8 EXERCISE
Recommendation: Adopt a personalized, moderate exercise plan; caution with over-training
Exercise alters metabolic methylation-related activity and biomarkers. According to a 2014

systematic review, daily activity is consistently associated with lower homocysteine levels in a
dose-dependent manner [141]. And in animal models, exercise has been shown to prevent folate
deficiency-induced hyperhomocysteinemia at least in part via increased BHMT expression
(two-fold) in the kidney [142]. Acute exercise, however, is associated with a temporary (<24
hour) increase in plasma homocysteine, especially in untrained individuals, which is thought to
be due to the increased catabolism of muscle proteins during exercise to make amino acids
available for gluconeogenesis in the liver [141], [143]. This acute effect can be exacerbated by
low folate and vitamin B12 status [144], making nutrient repletion important.
Exercise, especially regular and at moderate intensity, is an effective antidote to factors that can
deplete methyl donor reserves or negatively alter methylation activity, namely psychological
stress, oxidative stress and inflammation [145]. Aerobic exercise and resistance training are also
associated with increased cellular glucose uptake and reduced blood glucose [146], which
would also reduce oxidative stress caused by higher AGE-promoting glucose levels.

The enhanced production of reactive oxygen species and free radicals during acute exercise, as
well as increased levels of pro-inflammatory cytokines, is well documented [140], [147], but
long-term effects of these changes depends on the type of activity and duration of an active
lifestyle. Some caution is warranted with high-intensity or anaerobic exercise which may have
deleterious pro-oxidative effects, particularly in untrained individuals. Endurance exercise, for
example, may produce circulating levels of IL-6 that are up to 120 times that of baseline, as well
as localized increases in other predominantly pro-inflammatory cytokines [140]. And a 2013
systematic review, investigating the effect of exercise on levels of oxidative stress in the brain,
found that regular, moderate, aerobic exercise increases the brain’s antioxidant capacity, but
that high-intensity, anaerobic exercise could reduce the antioxidant response [148]. These
discrepancies may be explained by a hormesis model of exercise (Figure 6), which argues that
too little or too much exercise can produce negative effects [149]. Gradual build-up of exercise,
via regular practice or training, can shift the hormesis curve to the right, meaning that exercise
tolerance and benefits are highly personalized.
Figure 6: Hormesis and Exercise [149]. Used with permission.
It has been argued in recent reviews that abundant dietary antioxidants provided by a diet rich
in natural plant phytochemicals (vegetables, fruits, whole grains, legumes and beans, sprouts
and seeds) are an effective way to meet the antioxidant requirements of physically active
individuals and athletes [147], [149]. In fact, dietary intervention may well be a more effective

strategy than antioxidant supplementation, since a studies using supplementation show

insufficient and mixed results, and some researchers even theorize that antioxidant
supplementation may blunt the beneficial hormetic effects of exercise and delay muscle
recovery [147], [149].
Both acute and chronic exercise do appear to induce changes in DNA methylation, according to
a recent review of literature [150]. For example, in a retrospective study of 647 women, regular
exercise throughout a lifetime appears to act to preserve the age-related depletion of global
methylation status:, physical activity (including sports, and also daily movement such as
climbing stairs, housework, and yardwork) that was greater or equal to the median in three
distinct life stages (childhood, adolescence, and adulthood), did have small, but significant,
increases in global DNA methylation compared with those who did not meet that level of
physical activity in all three life stages [151]. Women who practiced physical activity at or above
the median in only one or two of those life stages also had increased DNA methylation, but
statistical significance was lost. The median level of exercise was calculated as 9.8 hours per
week in childhood, 5.9 hours per week in teenage years, and 12.5 hours per week in adulthood.
In a separate case-control study of 500 females, long-term tai-chi practitioners (at least one hour
per week for 3 years or more) demonstrated a slowing of age-related DNA methylation losses,
of between 5-70%, compared with controls [152]. During their research, the investigators
determined that a significant difference in methylation between the two groups at a number of
specific sites only occurred after 50-55 years of age, leading to their speculation that tai-chi may
be of particular benefit in this age-group.
Although the mechanisms of the effects of exercise on DNA methylation are not yet well
understood, theories speculate that this may be mediated by the inflammation-lowering effect
of exercise, or via altered sex hormone levels that then in turn alter DNA methylation [150].
Mind-body exercises such as tai-chi may also be beneficial due to their effects on stress hormone
levels and stress responsiveness.
7.9 NUTRACEUTICAL INTERACTIONS

Recommendation: Understand the potential interactions with long term supraphysiological
supplementation of niacin, selenium, and phosphatidylethanolamine
As most of us have witnessed, nutraceutical supplements used in functional and integrative
medicine, and nutrition practice, have powerful effects on physiology. Indeed, they are one of
the primary tools that practitioners use to help their patients achieve optimal wellness.
However, it behooves the practitioner to be aware of potential interactions, and in this context
the ones that may negatively affect methylation.
Certain nutrients are metabolized in the body via methylation, specifically niacin, selenium and
phosphatidylethanolamine (Table 9). Therefore high dose supplemental regimens of these

nutrients may drain the pool of available methyl donors and either create or worsen a
methylation deficit. Niacin also limits pyridoxal kinase, which normally activates vitamin B6
[6], therefore high doses of this nutrient may impair vitamin B6 status.
Table 9: Nutrients metabolized via methylation
Caution with long term, high doses of these

nutrients that are metabolized via methylation
Niacin
Selenium
Phosphatidylethanolamine
7.10 MEDICATION INTERACTIONS

Recommendation: Caution with medications that alter the status of methylation nutrients
A number medications are known to impede methylation activity in distinct and specific ways.
Some medications may impair nutrient absorption, some inhibit enzyme function, and others
deplete SAMe (Table 11). An understanding and judicious use of these is imperative to
optimally preserve methylation function.
Table 10: Select medications that can inhibit methylation nutrients and pathways [6]
Medication(s) Effect
B12
Antacids and proton pump inhibitors B12 insufficiency
Cholestyramine Alters B12 and folate absorption
Colestipol Alters B12 and folate absorption
Metformin B12 malabsorption
Nitrous oxide Inactivates methionine synthase

B6
Niacin Depletes SAMe and limits pyridoxal kinase

which normally activates B6
Theophylline Limits pyridoxal kinase
Folate
Phenytoin Folate antagonist
Carbamezepine Folate antagonist
Antimalarials, pyrimethamine, proguanil Inhibit DHFR
Sulfasalazine Inhibits DHFR
Triamterene Inhibits DHFR
Methotrexate Inhibits DHFR
5-fluorouracil (5-FU) Inhibits thymidylate synthase
Oral contraceptives Increases folate requirements
Homocysteine clearance
Cyclosporin A Decreases renal function, increasing

homocysteine, increasing requirement for
conversion to methionine

8 THE METHYLATION DIET FOOD PLAN

A vital step in supporting methylation with food is to utilize a “Food Plan” that encompasses
the different nutrient requirements and limits or avoid factors that can negatively impact
methylation.
A Methylation Diet Food Plan should be nutritionally replete, anti-inflammatory, low-glycemic,
antioxidant rich, and supportive of detoxification processes. A balanced diet of vegetables,
fruits, legumes, nuts, seeds, complete proteins, and whole grains provides plentiful methylation
nutrients. Methylation “superfoods” including beets, spinach, sea vegetables, daikon radish,
shiitake mushrooms, salmon, fish roe, whitefish, oysters, eggs, pumpkin seeds, sesame seeds
and sunflower seeds provide high levels of methylation-specific nutrients. Organ meats such as
liver are also valuable, dense sources of relevant nutrients, especially the vitamins B2, B3, B6,
folate, choline and betaine.
Foods as DNA Methylation Modulators?
Food bioactive components can affect DNA methylation directly at the genetic level,
apparently with modulating effects that appear to be site selective and dose dependent.
For instance, a number of phytochemicals as well as selenium have been shown, using
high in vitro concentrations, to inhibit DNMT enzymes [39]. These include compounds
found abundantly in plant foods such as apigenin, betanin, biochanin A, caffeic acid,
catechin, chlorogenic acid, coumaric acid, curcumin, cyanidin, diadzein, ellagic acid,
epicatechin, epicatechin gallate, epigallocatechin, epigallocatechin 3-gallate (EGCG),
galangin, genistein, hesperidin, luteolin, lycopene, myricetin, naringenin, quercetin,
resveratrol, rosmarinic acid, and sulforaphane. The selective de-methylation of the
promoter regions in tumor suppressor genes is suggested to be one of the mechanisms
underpinning the anti-cancer effects of compounds such as genistein, anthocyanins and
green tea polyphenols [34], [166].
Food bioactives have been shown to modulate genetic expression in other contexts such
as Phase I and Phase II detoxification [167], and as such the inclusion of whole, colorful
and varied plant foods in the diet is likely to be of benefit not only for nutrient status,
anti-inflammatory and anti-oxidant benefit, but also directly for healthy DNA
methylation and epigenetic expression.

Oxidative stress can be further reduced in the diet by limiting food preparation techniques that
promote the formation of pro-oxidative advanced glycation end products [153]. Advanced
glycation end products form primarily in animal-derived foods cooked in high, dry heat. Their
formation can be minimized by cooking at lower heats and with moisture. Proper hydration is
also an important factor in reducing oxidative stress [154]. Phytonutrients may be valuable in
that they act as beneficial enzyme modulators [6], [155], [156] as well as antioxidants.
Controlled caloric restriction may be recommended since it is considered to slow or reverse the
age-related decline in global DNA methylation and has been shown to favorably modulate the
methylation of genes related to diseases such as cancer [157]. Coupled with a lower
carbohydrate diet, an extended nighttime fast (such as by completing all food intake by 7pm)
that stimulates the production of a low level of the ketone body, β-hydroxybutyrate, may also
have protective effects on the epigenome [158], [159], as well as significant anti-inflammatory
action [160]. While we do regularly use short-term, targeted ketogenic diets in clinical practice
for their effective anti-inflammatory and weight loss outcomes, it should be noted that a full
ketogenic diet, while used as an effective therapy for epilepsy and certain cancers [161], [162], is
not suitable for long-term methylation support without careful monitoring due to the restriction
on amino acid intake that can deplete methionine status [163].
Fortified grains should be reduced or eliminated, especially if methyl donor supplementation is
not tolerated. Alcohol is inadvisable since it produces unfavorable DNA methylation patterns
[5], may interfere with SAMe activity [89] and impedes folate metabolism [164] including via
inhibition of MTR enzymes [165].
Table 11: Principles for a Methylation Diet Food Plan
Dietary guidelines Foods dense in methylation-related

nutrients
Optimal hydration (half your body
weight in fluid ounces of non-
caffeinated beverages per day)
Varied, colorful plant foods

High fiber intake
Organic as much as possible
“Low and slow” cooking and raw

food

Low carbohydrate, especially if

insulin resistance or inflammation is
present
Consider caloric restriction
What to avoid Fortified grains

Alcohol
Added sugars
Foods from animals raised with
antibiotics
Foods from animals raised with

hormones
High-mercury fish, including tuna,
King mackerel, shark and swordfish
High-heat animal food preparations
such as grilling or deep frying
Plastic food and beverage containers
Further detail is outlined in Table 12, which specifies which foods to include, and which to
exclude. Bolded foods are especially notable for their contribution to methylation-related
nutrients. Bolded and capitalized foods are the most significant contributors to methylation-
related nutrients.

Case 2.0: Lowering homocysteine with a combination of supplements, diet and lifestyle
Susan felt that she had been healthy up until having her first child. Now, at 57 and postmenopausal, she
was recently diagnosed with latent autoimmune diabetes of adults (LADA), and Hashimoto’s thyroiditis.
Her blood glucose was 335 ng/dL, with an HbA1C of 12.1. Of course, our work with Susan was multi-
faceted, tailored to address the various underlying factors that related to these concerns.
Her initial program included a lower carbohydrate, anti-inflammatory diet and micronutrient for gut
repair, detoxification and blood sugar control. A modest methyl donor prescription included 400 mcg 5-
mTHF and 1000 mcg methyl-B12. At two months, Susan’s blood sugar was 108. However, her
homocysteine was 14.0. She was also identified as heterozygous for both the MTHFR 677 and 1298
mutations.. These findings prompted the initiation of our MDL program and a modestly increased methyl
donor prescription of 800 mcg 5-mTHF and 5000 mcg methylcobalamin.
Our nutritionist initiated a gluten-free, dairy-free, methylation Food Plan that also addressed her
ongoing needs for blood sugar control, curbing inflammation, and balancing immune function. She
helped Susan emphasize foods rich in methylation nutrients such as leafy greens, beets, daikon, shiitake,
spinach, seeds and high quality protein. One of the principle challenges for Susan was her frequent
business travel to Asia. Careful guidance for navigating restaurant food, as well as dry food supplies to
take with her for meal replacements and snacks as needed, helped with compliance. Guidance for
minimizing mercury exposure in food (her mercury levels initially showed high, and she did have some
remaining amalgams which would also be contributing to that result), as well as working through
strategies for “clean” living and stress management, rounded out her diet and lifestyle plan.
Four months later, labs are showing remarkable results. Her fasting blood glucose is down to 82 and her
homocysteine is at 7.1. She reports feeling very well, and is motivated to continue the program.

Table 12: The Methylation Diet Food Plan – Foods to Include and Exclude
Bolding identifies foods of particular relevance to the Methylation Diet; Bolding and capital letters
further identify some of the most important foods for the Methylation Diet
Category Eat this… Not this…
Vegetables Include a variety of colorful vegetables and fruits, 8-12 Deep-fried vegetables.
and fruits servings per day.
Potato chips, fries,
Red: apples (with skin), BEETS, bell peppers, processed vegetable
blood oranges, cranberries, cherries, grapefruit snacks.
(pink), goji berries, grapes, onions, plums,
pomegranate, radicchio, radishes, raspberries,
strawberries, sweet red peppers, rhubarb, rooibos
tea, tomato (including sun-dried tomatoes),
watermelon.
Orange: apricots, bell peppers, cantaloupe,
carrots, mango, nectarine, orange, papaya,
persimmons, pumpkin, squash (acorn, butternut,
winter), sweet potato, tangerines, turmeric, yams.
Yellow: apple, Asian pears, banana, bell peppers,
corn, ginger root, lemon, millet, pineapple,
starfruit, succotash, summer squash.
Green: apples, artichokes, asparagus, avocados,
bean sprouts, bell peppers, bitter melon, bok choy,
broccoli, broccoli sprouts, Brussels sprouts,
cabbage, celery, cucumbers, edamame, green
beans, green peas, greens (arugula, beet, chard,
collard, dandelion, escarole, kale, lambsquarters,
lettuce (endive, green, mesclun, raddichio, red,
romaine, spring), purslane, mustard, SPINACH,
turnip), kiwi, kohlrabi, leeks, limes, okra, olives,
parsley, pears, snow peas, sea vegetables (agar,
kelp, SPIRULINA, wakame),watercress,
zucchini.
Blue/purple/black: bell peppers, berries (blue,
black, boysenberries, huckleberries,
marionberries), cabbage, carrots, cauliflower,
eggplant, figs, grapes, kale, kohlrabi, olives,

plums, potatoes, prunes, raisins, rice (black or

purple).
White/brown: cauliflower, celeriac, DAIKON
RADISH, garlic, horseradish, mushrooms
(including SHIITAKE), onions.
Animal Include, but in moderation (6-10 oz/day, based on 0.8 Chargrilled, broiled or
protein grams of protein per kg body weight). deep fried meats and fish.
Fish (anchovy, bass, mackerel, sardines, Processed meats
SALMON, cod, FISH ROE, flatfish, halibut, including sausage, cold
haddock, herring, perch, snapper, squid, tilefish, cuts, canned meats,
trout, WHITEFISH), shellfish (clams, crab, frankfurters.
lobster, mussels, octopus, OYSTERS, scallops,
shrimp), venison, beef, bison, buffalo, lamb,
duck, elk, goose, skinless chicken, Cornish hen,
turkey, pork, rabbit, quail. Organ meats such as
LIVER, tongue, marrow, sweetbread. EGGS
including chicken, duck and goose.
Fish in italics are good low-mercury, high omega-3
choices. Grass-fed/wild animal products are leaner and
have higher omega-3 content. Choose eggs that are
omega-3 enriched.
Nuts & seeds Almonds, Brazil nuts, black walnuts, butternuts,

cashews, chestnuts, coconut, hazelnuts, peanuts,
pecan nuts, pine nuts, pistachio nuts, walnuts.
Chia seed, flaxseed, hemp seed, poppy seeds,
PUMPKIN SEEDS, SESAME SEEDS,
SUNFLOWER SEEDS, watermelon seeds.
Oils Choose cold-pressed and unfiltered: Olive, flaxseed, Margarine, shortening,

coconut, sesame, almond, sunflower, safflower, hydrogenated fats,
avocado, red palm, walnut, and pumpkin seed vegetable oils, processed
oils. Grass-fed butter and ghee. Cook with butter, oils.
coconut oil, ghee, olive oil, or red palm oil.
Spices and All spices and herbs including salt, black pepper,
herbs anise seed, basil, bay leaf, cardamom, carob,
cayenne pepper, celery seed, chervil, cilantro
(coriander leaf), cinnamon, chili powder, cloves,

coriander seed, cumin, dill, fennel seed,

fenugreek, garlic, ginger, marjoram, mustard,
oregano, paprika, parsley, rosemary, saffron,
sage, savory, spearmint, tarragon, thyme,
turmeric.
Condiments Baker’s yeast, brewer’s yeast, cocoa (70%+ dark, Store-bought condiments
not Dutch processed), coconut aminos, mustard, with sugar and additives.
salsa (sugar-free), tamari/soy sauce (low sodium),
vinegars.
Drinks Pure water (filtered, mineral or distilled), coconut Alcohol, fruit juices and
water, herbal teas such as mint, chamomile, green, soft drinks.
hibiscus, and Rooibos.
Maximum 1-2 cups per day of caffeinated
beverages (optional).
Dairy Dairy and eggs (high quality sources): Milk, Ice-cream, sweetened
cheese, eggs, cottage cheese, cream, yogurt (no yogurts, frozen yogurt,
sugar added), butter, cow’s milk kefir, gruyere non-dairy creamers.
cheese, goat cheese, parmesan cheese, Romano
cheese.
Unsweetened, non-dairy milks including almond,
cashew, coconut, and hemp milks. Coconut milk
kefir.
Vegetable Fermented soy such as tempeh, miso, tamari, Other soy products: soy
protein natto, pickled tofu. Legumes including beans sauce, tofu, soybean oil in
(adzuki, black, cannellini, fava, garbanzo, great processed foods; soymilk,
northern, kidney, lima, mung, navy, pinto, red, soy yogurt, textured
turtle), black-eyed peas, hummus, lentils, split vegetable protein.
peas.
Grains Whole grains, preferably soaked and even Any flour-based products
sprouted before cooking, including amaranth, including breads, pastries
barley, buckwheat, bulgur, corn, kamut, millet, and cookies.
quinoa, oats, rice (basmati, bran, brown, wild),
rye (including dark rye), sorghum, spelt, tapioca,
teff, wheat.

Sweeteners Very limited amounts of blackstrap molasses, Refined sugar, high

honey, maple syrup, stevia or unrefined cane fructose corn syrup,
sugar allowed if needed. evaporated cane juice,
artificial sweeteners.
Support for the implementation of the MDL Food Plan is important to continue to ensure
desired levels of nutrient intake. Even ‘healthy’ diets can be lacking in nutrients, or fail achieve
sufficient therapeutic nutrient levels if they are implemented incorrectly. To that end, we have
created two sample menu plans that may be used, along with more than 45 recipes. We also
recommend regular nutrient intake analysis, especially in the early stages of implementation, to
elucidate any adjustments that may be needed.

9 MENU PLANS
9.1 SAMPLE MENU 1: GLUTEN-FREE, DAIRY-FREE

Breakfast Lunch Dinner Snack Smoothie/Juice
Mon Eggs with Swiss Chicken Caesar Beef and Vegetable Roasted Spiced Sea Green Smoothie
Chard Salad Stir-Fry with Brown Chickpeas
Rice
Tue Chia-Berry Pesto-Vegetable Warm Artichoke, Pâté with Berry Bliss

Creamy Cereal Frittata Tomato and Chicken Cucumber Smoothie
Salad “Chips”
Wed Cranberry- Borscht with Turkey Meatballs Nutty Snack Balls Sweet and Spicy
Apple-Cinnamon Seaweed Salad with Roasted Juice
Oatmeal Vegetables
Thu Hardboiled Eggs, Warm Quinoa Red Lentil and Hazelnut Butter Sea Green Smoothie
Sunflower Seed Salad with Wild Tempeh Curry with and Apple Slices
Hummus and Salmon and Brown Rice; Steamed
Avocado Asparagus Bok Choy
Fri Grain and Nut Whole Beet Salad Lamb Curry; side of Nori Chips Ginger Greens Juice
Hot Cereal with Cashew Simple Vegetable Stir
Dressing Fry
Sat Root Veggies and Colorful Quinoa- Mackerel with Truffle Treats Berry Bliss
Poached Eggs Lentil Salad Ginger-Lime Smoothie
Marinade; side of
Creamy Coconut
Collards
Sun Turkey Breakfast Kale and Crispy Cauliflower Baked Hazelnut Butter Zesty Beet Juice
Sausage with Chickpea Salad Eggs with Daikon and Apple Slices
Chard and Fruit and Dulse Salad
Medley

9.2 SAMPLE MENU 2: PALEO

Smoothie/Juice
Breakfast Lunch Dinner Snack
Mon Eggs with Swiss Chicken Caesar Beef and Vegetable Nori Chips Sweet and Spicy
Chard Salad Stir-Fry with Juice
Cauliflower Rice
Tue Chia-Berry Creamy Pesto-Vegetable Warm Artichoke, Hazelnut Sea Green

Cereal Frittata Tomato and Chicken Butter and Smoothie
Salad Apple Slices
Wed Salmon Cakes with Borscht with Turkey Meatballs Nutty Snack Sweet and Spicy
Cantaloupe Melon Seaweed Salad with Roasted Balls Juice
Vegetables
Thu Hardboiled Eggs, Cauliflower- Grilled Beef and Pâté with Sea Green
Sunflower Seed Celeriac Soup Vegetable Skewers Cucumber Smoothie
Hummus (Paleo with Basil Dressing; “Chips”
version) and Steamed Bok Choy
Avocado
Fri Fruit Medley with Whole Beet Salad Lamb Curry; side of Nori Chips Power Protein
Nuts with Cashew Simple Vegetable Stir Smoothie
Dressing Fry
Sat Root Veggies and Warm Cauliflower Mackerel with Truffle Ginger Greens
Poached Eggs Couscous with Ginger-Lime Treats Juice
Wild Salmon and Marinade; side of
Asparagus Creamy Coconut
Collards
Sun Turkey Breakfast Kale and Cranberry Cauliflower Baked Hazelnut Zesty Beet Juice
Sausage with Chard Salad Eggs with Daikon Butter and
and Fruit Medley and Dulse Salad Apple Slices

9.4 MENU NUTRIENT ANALYSES
Both menu plans above provide ample methylation nutrients (Table 14). In our practice, we also
find it prudent to conduct periodic nutrient intake analyses on patients following a long-term
Methylation Diet and Lifestyle, to ensure that individuals are able to maintain that intake
beyond just one week.
Table 14: Average daily methylation-related nutrient intake of Sample Menus
Nutrient Sample Menu 1 Sample Menu 2 RDA (adult male/female)
(Daily Average) (Daily Average)
Folate 625 mcg 626 mcg 400/400 mcg DFE1
Folic acid 0 mcg 0 mcg 400/400 mcg DFE1
Vitamin B12 4.8 mcg 5.6 mcg 2.4/2.4 mcg
Betaine 321 mg 233 mg -
Choline 455 mg2 414 mg2 550/425 mg
Riboflavin (Vitamin B2) 1.8 mg 1.9 mg 1.3/1.1 mg
Niacin (Vitamin B3) 19 mg 22 mg 16/14 mg
Vitamin B6 2.7 mg 2.8 mg 1.3/1.3 mg
Zinc 13.4 mg 13.9 mg 11/8 mg
Magnesium 605 mg 569 mg 420/320 mg
Omega 3 fatty acids 5.3 g 4.9 g -
Total calories 1792 kcal 1743 kcal -
% calories from 35% 30% -
carbohydrates
% calories from fats 47% 52% -
% calories from protein 18% 18% -

1Dietary folate equivalents
2Actual choline intake is underreported since many foods in the USDA database have not been evaluated for choline content

10 RECIPES

BREAKFAST

Eggs with Swiss Chard
Servings: 1
Cook time: 10-15 minutes
• 3 organic, omega 3 eggs prepared any style
For the Swiss chard:
• 1 tablespoon olive oil

• 1 clove garlic, crushed
• 6 cups Swiss chard leaves, stalks removed, roughly chopped into large pieces
• 1/4 teaspoon salt
• Black pepper, to taste
• 1/4 fresh lemon
Heat oil in a sauté pan over medium heat. Add garlic and cook for 2-3 minutes, taking care that
it does not burn. Add chard, salt and pepper and continue to cook on medium heat until wilted,
about 3-5 minutes. The excess liquid from the chard can be drained. Serve the Swiss chard
alongside the eggs, with a squeeze of lemon on the top. Adjust seasonings if necessary.

Chia-Berry Creamy Cereal
Servings: 1
Cook time: 5 minutes plus overnight soaking
• 3/4 cup water

• 1 tablespoon sunflower seeds
• 1 tablespoon flaxseeds
• 2 tablespoons chia seed
• 1/2 cup mixed raspberries and blueberries
• Sweetener of choice (such as stevia, coconut sugar, or lucuma), optional
• 1/4 teaspoon cinnamon
Blend almond milk, sunflower seeds and flaxseeds in a high-speed blender until creamy. Soak
chia seeds overnight in the milk/seed mixture. In the morning, add berries and sweetener and
top with cinnamon.

Cranberry-Apple-Cinnamon Oatmeal
Servings: 2
Cook time: 20 minutes, plus overnight soaking for the oats
• 1 teaspoon olive oil or coconut oil

• 1 cup steel-cut oats or thick-cut rolled oats*
• 2 cups water
• 1 apple, diced
• 1/2 cup fresh (not dried) cranberries (if using dried cranberries use only 1/4 cup)
• Dash of cinnamon, to taste
• Pinch of salt
• 1/4 cup walnuts for topping
• 1/2-1 teaspoon maple syrup/raw honey, optional
*Soak oats overnight before using.
Heat the oil/butter for a couple of minutes. Add the oats to the oil and stir to coat (toasting gives
the oats more flavor and helps it from getting clumpy.)
Add the 2 cups of water and cover pot, allow to boil up and simmer on low for 5-7 minutes.
Add apples, cranberries, cinnamon and salt, and stir oatmeal well. Continue to simmer on low-
medium heat for another 5-10 min, stirring occasionally. Remove from heat when the liquid is
absorbed and it reached the consistency you like. Top with walnuts and maple syrup or honey.

Hardboiled Eggs, Sunflower Seed Hummus and Avocado
Servings: 4, with some leftover hummus
Cook time: 10 min, plus extra for roasting the sunflower seeds
For the hummus:
• 1 15 oz. can chickpeas (drained)*

• 1 cup sunflower seeds (roasted)
• 3 tablespoons tahini (sesame paste)
• 3 cloves garlic
• 1/3 cup olive oil
• juice of lemon (2 or whole)
• 2-4 tablespoons water
• Sea salt and fresh pepper to taste
For serving:
• 8 organic, omega 3 eggs, hard boiled

• 1 ripe avocado, sliced
• 2 handfuls of baby spinach
*For a Paleo/low-lectin version substitute 1 cup canned pumpkin puree
Combine all hummus ingredients in a food processor or blender and process to a smooth paste.
This may take five minutes or so. Add more liquid slowly if necessary and check seasonings.
Best if chilled before serving.
Serve each person 2 eggs with 2 tablespoons of hummus and 1/4 avocado, on a bed of spinach.

Grain and Nut Hot Cereal
Servings: 2
Cook time: 20 minutes, plus overnight soaking
• 1 teaspoon coconut oil

• 1/2 cup steel-cut oats or thick-cut rolled oats (not instant)*
• 1/2 cup quinoa*
• 1/2 cup coconut milk
• 1 1/2 cups water
• 1/4 cup chia seeds
• Pinch of salt
• 2 tablespoons sunflower seeds (hulled), roughly chopped
• 2 tablespoons almonds, roughly chopped
*Soak oats and quinoa overnight before using
Heat the oil/butter for a couple of minutes. Add oats and quinoa to oil and stir to coat oats
(toasting gives the oats more flavor and helps keep it from getting clumpy).
Add the 2 cups of liquid and cover pot, allow to come to a boil. Reduce heat, remove cover and
add chia seeds, cinnamon and salt. Stir in. Continue to simmer on low-medium heat for another
5-10 min stirring occasionally. Remove from heat when the liquid is absorbed and it reached the
consistency you like. Before serving top or mix in sunflower seeds and nuts.

Root Veggies and Poached Eggs
Servings: 4
• 3 tablespoons olive oil

• 1 large onion, chopped
• 3 cloves garlic, minced
• 1 teaspoon fresh ginger, minced (or 1/2 teaspoon ground)
• 1 teaspoon ground cumin
• 1 teaspoon turmeric
• 1 teaspoon chili powder (reduce or eliminate if you prefer less spicy)
• 1/2 teaspoon Cayenne pepper
• 1 teaspoon sea salt plus 2 tablespoon for cooking the eggs
• 2 lbs mixed root vegetables (celeriac, rutabaga, parsnip, beets), peeled and cut into
1/2 inch cubes
• 1/2 cup tomato puree
• 1 1/2 cups chicken stock
• 1 tablespoon mild tasting vinegar, such as rice vinegar
• 8 eggs (organic, omega 3)
• 2 tablespoons dulse sea vegetable flakes
Heat oil over med-low heat. Add onion and cook for 6-8 minutes, until it begins to soften. Add
garlic and ginger and cook for an additional minute. Stir in additional spices and 1 teaspoon sea
salt, then add the cubed root veggies, tomato puree and stock. Stir then cover and allow to
simmer for an additional 10-15 minutes (until the root vegetables are tender). Stir frequently.
While that cooks, poach the eggs. Bring a large saucepan 2/3 full of water to a simmer. Add the
vinegar and 2 tablespoon salt to the water. Gently crack the eggs into a measuring cup, then
ease them into the water one at a time. Depending on the size of your pan, you will need to
work in batches to give each egg enough room. After four minutes (if you like the yolk still a
little soft), remove carefully with a slotted spoon. Serve 2 eggs on a large spoonful of root
vegetables. Sprinkle with dulse flakes.

Turkey Breakfast Sausage with Chard and Fruit Medley
Servings: 4 (makes 12 patties)
For the sausage:
• 1 1/2 lb. ground turkey breast

• 1/2 cup finely diced dried cherries
• 1 small onion, minced
• 1 tablespoon fresh sage, minced
• 1 tablespoon thyme, minced
• 3 tablespoons extra-virgin olive oil
• 3/4 teaspoon sea salt
• 1/2 teaspoon freshly ground black pepper
For the Swiss chard:
• 1 tbsp olive oil

• 8 cups Swiss chard, stems removed and torn into pieces
• Salt and pepper, to taste
For the fruit medley
• 1 cup berries (blueberries, raspberries, blackberries)

• 1/2 cup apple, diced
• 1/2 cup cantaloupe melon, cubed
In a large bowl, mix together the turkey, cherries, onion, sage, thyme, 1 tablespoon of the extra-
virgin olive oil, salt, and pepper until thoroughly combined. Divide and form the mixture into
12 patties.
Heat the remaining 2 tablespoons of extra-virgin olive oil in a nonstick skillet over medium
heat. Cook the patties for about 5 minutes each side, until fully cooked through.
For the Swiss chard, heat the oil in a large skillet or saucepan. Rinse the leaves, then add them,
still slightly wet, directly to the pan and steam/sauté for about 5-10 minutes until wilted. Season
to taste.
For the fruit medley, simply combine the fruits together and serve a 1/2 cup serving alongside
the sausage patties and Swiss chard.

Salmon Cakes
Servings: 4 (approximately 12 cakes)
Cook time: 45 minutes
• 1 medium sweet potato, baked whole then flesh scooped out and reserved
• 1/3 cup coconut flour
• 1 clove garlic, minced
• 1/2 onion, finely chopped
• 1/4 cup red bell pepper, finely chopped
• 1/4 cup cilantro or parsley, finely chopped
• Juice of 1/2 lemon
• 1 teaspoon Cayenne pepper
• 1 teaspoon salt
• 2 eggs
• 2 x 6 oz-ounce cans Wild Alaskan Pink Salmon, skinless and boneless, flaked
Preheat the oven to 400° and line a baking sheet with parchment paper
Combine all ingredients in a large bowl and mix thoroughly.
Form the mixture into 12 patties of roughly the same size. Using a 1/3 cup measure can be
helpful for this!
Place on the baking sheet and cook in the oven for 20-25 minutes, until turning golden brown.
Remove from the oven, turn over with a spatula, and return to the oven to cook for 10 minutes
more.

Fruit Medley with Nuts

Servings: 1
• 1 cup berries (blueberries, raspberries, blackberries)

• 1/2 cup apple, diced
• 1/2 cup cantaloupe melon, cubed
• Add 1/4 cup cashews, almonds, or mix of both
Toss all ingredients together and serve immediately.

LUNCH

Chicken Caesar Salad
Servings: 4
Cook time: 30 minutes, plus extra for preparing the chicken
For the chicken:
• 4 x 3 oz chicken breasts (or two large, divided)

• 4 cloves garlic, crushed
• 1 tablespoon lemon juice
For the dressing:
• 2 organic egg yolks

• 2 tablespoons lemon juice
• 1 tablespoon Dijon mustard
• 1 tablespoon minced anchovy fillets
• 1/3 cup olive oil (extra virgin)
• 3 garlic cloves, minced or pressed
• Sea salt and ground black pepper to taste
For the salad:
• 10 cups romaine lettuce, washed and torn into bite sized pieces
Set the oven to 375°F. Marinade 2 chicken breasts in olive oil, crushed garlic and lemon juice for
a couple of hours. Bake for 20 minutes until cooked all the way through. Set aside and allow to
cool. Slice into pieces or cubes.
Make the dressing: Mash 1 small garlic clove and a pinch of kosher salt until reduced to a paste
(mortar and pestle is best, but you can improvise with knife or spoon). Add anchovies, continue
to mash and chop until well combined and nearly smooth. Move to a medium bowl, and whisk
in Dijon mustard, then the egg yolks, followed by lemon juice. Blend well. Slowly, drop by
drop, add olive oil whisking constantly until dressing is thick and glossy. If desired add more
sea salt, freshly ground black pepper, and more lemon juice.
In a large bowl, toss the lettuce, chicken and dressing until everything is evenly coated. Serve
immediately.

Pesto-Vegetable Frittata
Servings: 4
For the pesto: For the frittata:
• 2 cups fresh basil leaves • 1 tablespoon coconut oil

(packed) • 1 medium onion, finely sliced
• 1/2 cup fresh parsley leaves • 1 cup shitake mushrooms, sliced
(packed) into small pieces
• 2 garlic cloves • 3 cups broccoli, chopped into small
• 1/3 cup olive oil pieces
• 1/2 cup walnuts • 6 eggs (organic)
• Sea salt • 2 tablespoon ground golden flaxseed
• Black pepper mixed with 6 tablespoons water
• 1/4 teaspoon oregano
• 1/4 teaspoon thyme
• Sea salt and fresh black pepper to
taste
First make the pesto: In a food processor, blend basil, parsley, garlic and walnuts together using
pulse setting till they’re well mixed. Slowly add in olive oil and continue blending until smooth.
Season with sea salt and black pepper to taste.
Preheat the oven to 375˚F. Heat the oil in an oven safe skillet over medium heat, add the onion
and allow to soften for 5 min. Add the mushrooms and continue to sauté for another 5-10
minutes. Meanwhile, steam the broccoli for 3-4 min, then add to the skillet.
Beat 3 of the eggs with 1/4 teaspoon salt and pour into the same skillet containing the onions,
broccoli and mushroom. Stir briefly. Spoon about half of the pesto into the skillet but don’t stir
any more. Beat the remaining eggs with another 1/4 teaspoon salt, mix in the flax and water
mixture, then pour into the skillet.
Bake for 20 minutes, then broil for an additional 2 minutes. Allow to cool, then top with
remaining pesto and serve.
Follow with 1 cup cubed cantaloupe melon.

Borscht (Beetroot Soup)
Servings: 4
• 1 tablespoon olive or coconut oil

• 1 yellow onion, chopped
• 4 garlic cloves, peeled and smashed
• 1 bay leaf
• 6 cups beets, peeled and cubed
• 1.5 cups carrots, peeled and chopped
• 1/3 cup cashews
• 3 cups vegetable or chicken stock
• 1/2 teaspoon sea salt and black pepper to taste
• Fresh chives for garnish, chopped
In a large saucepan, heat the garlic and onions in the oil for about 10 minutes. Add the bay leaf,
beets, carrots, cashews and stock. Bring to a simmer and stir. Add more liquid if needed to just
keep the vegetables covered. Allow to cook on low, covered, for 30 minutes, until the beets and
carrots are soft. Add the lemon, salt and pepper.
Remove the bay leaf, then puree the soup with an immersion blender, or in batches in a high-
speed blender. Garnish, and serve.

Warm Quinoa Salad with Wild Salmon, Asparagus and Kale
Servings: 4
• 1.5 lb wild salmon filet

• 1 red bell pepper
• 2 tablespoons pine nuts
• 3/4 cup quinoa, soaked for at least 20 minutes, then rinsed well (will yield 1 1/2 cups
cooked)
• 2 cups asparagus, cut into thirds
• 6 cups kale, wash and trim heavy stems, torn into pieces
• 1 tablespoon fresh chives, chopped
• 2 tablespoon fresh parsley, chopped
• 2 teaspoons lemon juice, freshly squeezed
• 1 teaspoon tahini (sesame seed butter)
• 3 tablespoons water
• Salt and freshly ground black pepper
Heat the oven to 400F. Line a baking sheet with parchment paper. Season the salmon lightly
with salt and bake with the red bell pepper (whole) for 20-25 minutes. Add the pine nuts for the
last 5-7 minutes of baking.
Meanwhile, bring the quinoa to a boil in plenty of salted water (3 cups), and simmer for 10-12
minutes until tender (the quinoa seeds will uncurl and will be just soft to taste). Drain and
return to the pan, covered. Let sit for 5-10 minutes.
In a separate saucepan, cover and cook the asparagus in an inch of water until tender, about 10
minutes. Right before removing, add the kale and cook for another minute or two until it wilts.
Drain and set aside.
In a small bowl, make the dressing: whisk the chives, parsley, lemon juice, tahini and water
together until smooth. Add salt and pepper to taste.
Assemble your warm salad: Flake the salmon into a bowl. Chop the red pepper (removing the
stalk and seeds) and add that too. Add the pine nuts, quinoa, asparagus and dressing. Toss to
combine everything.

Warm Cauliflower Couscous Salad with Wild Salmon, Asparagus and Kale (Paleo
version)
Servings: 4
• 1.5 lb wild salmon filet

• 1 red bell pepper
• 1 head cauliflower
• 2 tbsp dried parsley
• 2 cups asparagus, cut into thirds
• 6 cups kale, wash and trim heavy stems, torn into pieces
• 2 teaspoons lemon juice, freshly squeezed
• 1 teaspoon tahini (sesame seed butter)
• 3 tablespoons water
• Salt and freshly ground black pepper
Heat the oven to 400F. Line a baking sheet with parchment paper. Season the salmon lightly
with salt and bake with the red bell pepper (whole) for 20-25 minutes. Add the pine nuts for the
last 5-7 minutes of baking.
Meanwhile, prepare the other ingredients:
Chop the cauliflower into large chunks and pulse in the food processor until the texture
resembles couscous. Be careful not to over process. Heat a sauté pan over medium heat and
gently fry the cauliflower together with the parsley, and some salt and pepper, stirring
frequently, until tender, about 5-7 minutes. Take off the heat and set aside.
In a separate saucepan, cover and cook the asparagus in an inch of water until tender, about 10
minutes. Right before removing, add the kale and cook for another minute or two until it wilts.
Drain and set aside.
In a small bowl, make the dressing: whisk the chives, lemon juice, tahini and water together
until smooth. Add salt and pepper to taste.
Assemble your warm salad: Flake the salmon into a bowl. Chop the red pepper (removing the
stalk and seeds) and add that too. Add the pine nuts, cauliflower couscous, asparagus and
dressing. Toss to combine everything.

Whole Beet Salad with Cashew Dressing
Servings: 2
Cook time: 15 minutes for assembly, more for cooking beets and soaking cashews (can be done
the day before and kept refrigerated)
• 6 medium beets (buy with • 1/4 cup olive oil

leaves) • 1/4 cup walnuts, halved
• Beet leaves from those 4 beets,
trim heavy stems Dressing:
• 6-8 oz kale, wash and trim
• 1/3 cup cashews (soak for at
heavy stems, torn into bite-
least 1 hour prior)
sized pieces
• 2 cloves garlic
• 1 gala apple, cubed into small
• 1/4 cup apple cider vinegar
pieces
• 1/4 cup water
• 1/2 cup seedless grapes, halved
• Sea salt and ground black
• 1/2 red onion, chopped
pepper
• 2-3 celery stalks, diced
• 3 tbsp fresh parsley, chopped
Roasting beets (this can be done up to 36 hours beforehand and kept refrigerated): Preheat oven
to 350 degrees F. Place rack in middle of oven. Prepare the beets by trimming the stems
(reserve) and ends. Scrub well and cut in half. Toss with olive oil (enough to coat lightly). Place
the beets in an oven-proof dish (with a tight-fitting lid, or covered with aluminum foil, sides
pinched to seal), and add 1/2 an inch of water to the bottom of the dish.
Cover the beets and roast in the oven for 1-2 hours (depending on the size of the beets) until
tender. Remove from the oven and set aside to cool. Once cooled enough to handle, peel the
skin by hand or using a knife.
Prepare the dressing: Blend the dressing ingredients in a high power blender or food processor
until completely smooth and not grainy. Set aside.
Assemble the salad: In a large mixing bowl, combine greens, roasted beets, walnuts and other
fruits and veggies. Add dressing and toss well. Serve immediately.

Colorful Quinoa-Lentil Salad
Servings: 3
• 1 cup lentils*
• 1/2 cup quinoa*
• 1 cup water
• 1 cup vegetable broth
• 1 tablespoons extra virgin olive oil, plus extra for drizzling
• 1 lemon, juiced
• 1-2 cloves garlic, pressed
• 1/4 teaspoon cumin
• 1/4 teaspoon dried ginger
• Salt and pepper to taste
• 1 red pepper, diced
• 1/4 red onion, diced
• 2 medium carrots, grated
• 3 omega 3 eggs, hard boiled, roughly chopped
• 3/4 cup parsley, roughly chopped
• 3 cups arugula
*Soak, together, overnight before cooking.
In a pot, bring the water and broth to boil. Add quinoa and lentils and reduce heat to simmer.
Allow to cook for about 12-15 minutes until both are soft. Stir occasionally. When done, cover
and set aside to cool.
In a large mixing bowl, stir together the olive oil, lemon juice, garlic, cumin, ginger, salt and
pepper. Add the red pepper, onion, carrot, eggs and parsley and toss with the dressing.
When the quinoa and lentils have cooled, add to the veggies and mix thoroughly. Divide the
arugula between two plates and top with the quinoa-lentil salad. Drizzle with extra olive oil.

Kale and Crispy Chickpea Salad
Servings: 2
Crispy chickpeas Dressing
• 1 can (15 oz) chickpeas (garbanzo • 1 small head of garlic, whole, roasted
beans), rinsed, drained and with the chickpeas (see below)
thoroughly dried • 1/4 cup tahini (sesame seed paste)
• 1 tablespoon avocado oil • 1 tablespoons extra virgin olive oil
• 1 tablespoon cumin • 1/2 cup lemon juice (from approximately
• 1/2 teaspoon garlic powder 2-3 lemons)
• 1/2 teaspoon ground ginger • 2 tablespoons raw honey
• 1/2 teaspoon Cayenne pepper • Sea salt and pepper to taste
• 1/2 teaspoon paprika • Hot water
Other Ingredients
• 6 cups kale, chopped or torn into large pieces

• 2 omega 3 eggs, poached
Preheat oven to 375˚F.
Place the thoroughly-dry chickpeas in a mixing bowl. Add the avocado oil and chickpea
seasonings and toss to coat well. Transition to a baking sheet and spread out evenly. At this
point, also add the whole head of garlic (for the dressing) to the baking sheet, to roast alongside
the chickpeas. Bake for 18-25 minutes, until chickpeas are slightly crispy and golden. Remove
from oven and allow to cool.
Make the dressing: Slice the roasted head of garlic across-ways and squeeze out the garlic cloves
(they should come out easily when cooked). Add the garlic to a mixing bowl, along with the
remaining dressing ingredients. Using a fork, crush the garlic and whisk dressing ingredients
together. Adjust seasonings and add extra water as needed. Set aside.
In a large mixing bowl, add a small amount of dressing to the kale and massage with your
hands; this will help soften the kale. Add the remaining dressing (you may have extra left over),
and toss well. Divide the kale onto two plates, top with the chickpeas and poached eggs, and
serve.

Cauliflower-Celeriac Soup
Servings: 4
• 1 medium celeriac (celery root), skin trimmed and roughly chopped

• 1 medium cauliflower, cut into chunks
• 2 cloves garlic, peeled
• 1/4 cup cashews
• 1 small onion, peeled and quartered
• 1 cup unsweetened almond milk
• 4 cups chicken stock (homemade if possible)
• 1 teaspoon sea salt
• 1/4 cup fresh parsley, chopped
Place all ingredients except black pepper and parsley in a large, deep saucepan. Bring to a
boil and simmer for 20-25 minutes, until all the vegetables are tender. Let cool slightly and
then puree in a high-speed blender (best), or with an immersion blender. Thin with hot
water if necessary. Check seasonings and adjust as needed. Serve garnished with black
pepper and parsley.

Kale and Cranberry Salad
Servings: 2

• 1 tablespoons pumpkin seeds
• 5 cups kale, washed, large stems removed and torn into medium pieces
• 1 tablespoon flaxseed oil
• Juice of 1 lemon
• 1 teaspoon maple syrup
• Freshly ground black pepper
• 1/3 cup dried cranberries, soaked for at least 20 minutes
Set the oven to 350˚F. Toast the pine nuts and pumpkin seeds for 5-10 minutes, until fragrant.
Combine the kale with the oils, lemon juice, maple syrup, and salt and massage for a few
minutes to soften the kale and distribute the dressing. Add black pepper to taste.
Toss the kale with the cranberries and toasted pine nuts and pumpkin seeds.

DINNER

Beef and Vegetable Stir-Fry
Servings: 4
• 2 tablespoons coconut oil

• 1 tablespoon finely chopped fresh ginger
• 1 lb boneless sirloin steak, cut into 2-inch long thin strips (grass fed, organic if
possible)
• 2 cups Brussel sprouts, washed and quartered
• 1 medium onion, sliced into strips
• 1 red bell pepper, cut into strips
• 1 zucchini, diced
• 1 tablespoon apple cider vinegar
• 2 tablespoons fresh lemon juice
• Salt and black pepper, to taste
• 2 tablespoons sesame oil
• 2 tablespoons sesame seeds
• 3 tablespoon chopped cilantro
Heat a large skillet or wok over medium heat. Add 1 tablespoon coconut oil to the pan. Add
half the ginger and half the beef. Stir intermittently for about 2 minutes then transfer to a plate
in a warming oven. Repeat with another tablespoon. coconut oil and the remaining ginger and
beef.
Return the pan to the heat and add the remaining 1 tablespoon coconut oil. Add the Brussels
sprouts, onion, garlic, pepper and zucchini. Stir intermittently for 5-10 minutes. Add the
vinegar, lemon juice and return the meat to the skillet and stir together well. Season with salt
and pepper.
To serve, drizzle with sesame oil and sprinkle with sesame seeds and cilantro.

Warm Artichoke, Tomato and Chicken Salad
Servings: 1
• 1 tablespoon extra virgin olive or coconut oil (plus olive oil for drizzling)
• 1 clove garlic, finely chopped
• 1 cup artichoke hearts (frozen or water packed, drained)
• 1/3 cup cooked, shredded chicken (organic, free range if possible)
• 2 tomatoes, cut into 1-inch pieces
• 2 cups arugula
• 2 tablespoons pumpkin seeds
• 2 tablespoons sesame seeds
Heat the oil in a medium skillet over low heat. Add the garlic and cook 1-2 minutes, watching to
check it doesn’t burn. Add the artichoke hearts and chicken and cook 5-10 minutes more, until
fully heated through. Take off the heat, add the tomatoes and toss to combine. Season with salt
and pepper to taste.
Serve on a bed of arugula. Drizzle with olive oil and season with salt and pepper. Sprinkle the
seeds on top.

Turkey Meatballs
Servings: makes 12-16 meatballs (serves 2)
• 1 packet (1/2 lb) of ground turkey

• 1/2 cup nut flour (e.g. hazelnut, walnut) or ground seeds
• 3 tablespoons ground flaxseed
• 1 cup green leaves (choose the more tender varieties such as spinach, Swiss chard,
arugula)
• 2 tablespoons dried parsley
• 1 teaspoon onion powder
• 1/2 teaspoon garlic powder
• 1/4 teaspoon black pepper
Set the oven to 375˚F. Using a food processor, combine all ingredients until you have a near-
smooth mixture. If you don’t have a food processor, you can finely chop the greens, then mix all
the ingredients in a large mixing bowl until well-combined.
Form the mixture into about 12-16 meatballs, and place on (a) baking sheet(s) lined with
parchment paper. Bake for 15-25 minutes (for sizes 1-2” diameter) until cooked through.
These refrigerate and freeze well, and are great for snacking or adding to meals.

Red Lentil and Tempeh Curry
Servings: 4
Cook time: 1 hour

• 1 tablespoon ground cumin
• 1 teaspoon ground turmeric
• 1/2 teaspoon ground cinnamon
• 1/2 teaspoon ground coriander
• 1/4 teaspoon ground nutmeg
• 1/8 teaspoon ground clove
• 1 inch fresh ginger, peeled and grated
• 1 onion, minced
• 8oz packet of tempeh, crumbled
• 1 cup red lentils, debris removed and rinsed
• 2 cups vegetable stock
• 6 oz (1/2 a can) coconut milk
• 1 tbsp tahini (sesame butter)
• 2 teaspoons apple cider vinegar
• 1 teaspoon salt
For serving:
• 2 cups cooked brown rice

• 4 cups steamed bok choy
In a large saucepan, heat the oil and sauté the spices for 2-3 minutes until fragrant. Add the
onions and cook, stirring, for 5 minutes, until translucent. Add the garlic and tempeh and cook
for another 5-10 minutes. Add the remaining ingredients and simmer for 30-45 minutes. Add
water if more liquid is needed. You may also transfer to a slow cooker and cook on low for 6
hours. Check seasonings and adjust if necessary.
Serve with 1/2 cup cooked brown rice and 1 cup steamed bok choy per person.

Lamb Curry
Servings: 6

• 2 tablespoons curry powder
• 1/2 teaspoon turmeric
• 1/8 teaspoon cayenne pepper, or to taste
• 1 medium onion, chopped
• 1 1/2 lbs boned lamb shoulder, cubed
• 2 carrots, chopped into rounds
• 2 cloves of garlic, minced
• 2 teaspoons finely minced ginger
• 1/4 cup golden raisins
• 1 cup water
• 1 can (13.5 oz) full fat coconut milk
• Salt and pepper to taste
• 1/2 cup finely chopped fresh cilantro
Gently heat the oil in a large saucepan. First toast the spices until fragrant. Then add the onion
and sauté 2-3 minutes until starting to turn translucent. Add the lamb, carrots, garlic, and
ginger and sauté for a further 10-12 minutes. Add the raisins, water, coconut milk and
seasonings and bring back to a gentle simmer. Cook on low for 30 minutes until the lamb and
carrots are tender.
Check the seasonings, then stir in half the cilantro to wilt. Use the remaining cilantro for
dressing.

Mackerel with Ginger-Lime Marinade
Servings: 4
Cook time: 30 minutes, plus time to marinade.
• 1 lb Atlantic Mackerel fillets (not King Mackerel)

• 2 limes, zested and juiced
• 2 teaspoons fresh grated ginger
• 3 cloves garlic, crushed
• 2 tablespoons extra virgin olive oil
Rinse the mackerel and place, skin side up in a glass baking dish. Mix remaining ingredients in
a small bowl and stir/massage into the fillets. Cover, and marinade for 30 m to 2 hrs.
Preheat the oven to 400°F. Flip the fillets over. Cook for 15-25 minutes, until done. Extras can be
flaked, then refrigerated or frozen for easy additions to other meals.

Cauliflower Baked Eggs
Servings: 4
Cook time: 30-40 min
• 1 tablespoon coconut oil

• 6 eggs (organic, omega-3)
• 1/2 cup coconut milk
• 2 tablespoons ground flax seed mixed with 6 tablespoons water
• 1/8 teaspoon cumin
• 1 teaspoon sea salt
• 2 cups cauliflower, grated
• 1/3 cup onion, finely diced
• 1 leek, finely diced
For serving:
• 4 cups cantaloupe melon, cubed
Preheat the oven to 350˚F. Grease a 9 inch glass baking dish with the coconut oil (a pie dish
works well).
In a mixing bowl, beat the eggs and blend with the coconut milk, flax-water mixture, cumin and
sea salt. Add the cauliflower, onion, garlic and leek and stir well. Pour the mixture into the
baking dish and bake for 20-30 minutes until firm. Slice like a pie and serve with the melon

Grilled Beef and Vegetable Skewers with Basil Dressing
Servings: 2
Cook time: 25 minutes, plus more extra for marinating
For the marinade:

• Juice of 1 lemon
• 2 cloves of garlic, minced
• Freshly ground black pepper
For the skewers:
• 3/4 lb grass-fed sirloin steak, cubed

• 8-10 crimini mushrooms, larger ones halved
• 1 zucchini, sliced and cut into bite sized rounds
• 1 yellow summer squash, sliced and cut into bite-sized rounds
• 1 red bell pepper, stem and seeds removed, cut into bite-sized squares
For the dressing:
• 1 cup packed basil leaves

• 1/4 cup water or vegetable stock
• Sea salt to taste
For serving:
• 2 cups steamed bok choy
Combine the marinade ingredients in a large dish or bowl. Add the chopped beef and
vegetables and allow to marinade for at least 2 hours, up to 6.
Make up the skewers with the marinated beef and vegetables. Cook on a grill or grill pan over
medium-high heat for 4 minutes each side.
While the skewers cook, make the dressing: place the dressing ingredients in a food processor
(without the water/stock) or blender and process until smooth. With the motor running, slowly
add the water/stock until fully incorporated. Check seasonings.
Serve the skewers drizzled with the basil dressing, accompanied by steamed bok choy


SIDE DISHES

Basic Fluffy Quinoa
Start with white quinoa if you are new to the flavor. Red and black quinoa are also tasty
variations.
Serves: 6
Cook time: 25-30 minutes, plus soaking time
• 2 cups quinoa (yields about 6 cups cooked)

• 6-8 cups water
• 1 teaspoon salt
First you need to remove the bitter-tasting saponins from the quinoa. Soak the quinoa for at
least 20 minutes, and up to 12 hours. If you are planning to cook quinoa in the evening, setting
it to soak before leaving for work in the morning works well. After soaking, drain and rinse
well.
In a medium saucepan, bring the water to a boil. Add the quinoa and salt, and cook for about
10-15 minutes until the ‘grains’ have ‘opened’ and are just tender (start tasting them from 10
minutes). Drain all the water through a sieve, return the quinoa to the pan, and let sit (covered)
for 10-15 minutes.
Fluff with a fork and serve. Save any leftovers in the refrigerator or freezer. Quinoa is a perfect
base for adding flavors and more nutrients (such as herbs, garlic, spices, onion, sesame seeds) as
well as vegetables, legumes, and meats.
Variation in a rice cooker: Combine 1 cup soaked/rinsed quinoa with 2 cups water and 1/4 teaspoon salt
in the rice cooker; cook for 15 minutes.

Seaweed Salad
Servings: 4
Cook time: 15 min
• 2 oz dried assorted seaweeds or wakame (such as Eden Foods Brand)

• ¼ cup scallions
• 2 tablespoons coconut aminos
• 1 tablespoon apple cider vinegar
• ½ tablespoon sesame oil
• Pinch of cayenne pepper
• 1 tablespoon sesame seeds
In a large bowl, rinse and soak the seaweed in water enough to cover 10 times its volume. After
about 5 minutes, it should be tender, drain to remove excess water.
While the seaweed is soaking, make the dressing. Combine the scallions and remaining
ingredients in a small bowl and stir well.
Sort through the seaweed to make sure there aren’t any hard parts and cut it if it’s excessively
long (kitchen shears are useful for this task). Pour in the dressing and toss well to combine.

Roasted Vegetables
Servings: 2
Cook time: 45 min
• 1 cup carrots, peeled and sliced into 1-inch pieces

• 2 cup Brussels sprouts, tough outer leaves and stems removed, larger ones halved
• 1 head of garlic, cloves separated, and peeled
• 2 tablespoons coconut oil, melted
• 2 tablespoons Italian herb seasoning (rosemary, oregano, thyme, marjoram)
• ½ teaspoon salt
Preheat oven to 400˚F. Place the veggies and garlic in a large mixing bowl, add oil and
seasoning. Mix so that everything is coated evenly. Spread flat on a roasting pan or baking
sheet. Roast for 15 minutes, then mix and turn as much as possible, then roast for another 10-15
min. When the garlic and Brussel sprouts brown a little, and the carrots are tender, then they’re
done.

Simple Vegetable Stir Fry
Servings: 2 as a main course, 4 as a side dish
• 1 tablespoon sesame oil

• 1/2 teaspoon sesame seeds
• 3-4 cloves of garlic, minced
• 1/2 teaspoon cayenne pepper (optional)
• 2 cups Shiitake mushrooms, stems removed and sliced
• 1/2 head of cabbage, sliced into thin strips
• 8 cups bok choy, chopped
• Sea salt and freshly-ground black pepper
Heat the oil in a large sauté pan. Add the sesame seeds, garlic, and cayenne pepper. Toast the
seeds and spices in the oil for 1-2 minutes. Add the veggies one at a time, starting with the
mushrooms (cook 3-4 minutes until browning), then the cabbage, then bok choy. Cook, stirring
until just softened - the ends of the leaves will wilt. You’ll want them al dente, but not
overcooked. Add the chives and toss to combine. Season to taste with salt and pepper.

Creamy Coconut Collards
Serves: 4
• 1 tablespoon coconut oil

• 1/2 onion, diced
• 2 lb collard greens, large stems removed, washed and torn into large pieces
• 1/2 cup full fat coconut milk
• 2 tablespoons coconut aminos
• 1/2 teaspoon red pepper flakes (optional)
• 1/2 lemon
• Sea salt, to taste
Heat the coconut oil in a large sauté pan on medium heat. Gently cook the onions for 2-3
minutes, stirring intermittently, until starting to turn translucent.
Place remaining ingredients into the pan and continue to cook, stirring, until the collards wilt
and the liquid reduces (about 10 min). Check seasoning, squeeze the juice of 1/2 lemon over the
greens, and serve.

Cauliflower ‘Rice’
Servings: 4
• 1 head of cauliflower, roughly chopped into medium sized pieces

• 4 tablespoon extra virgin olive oil
• 1 teaspoon salt
Place the cauliflower into a food processor and pulse until the texture resembles rice.
Heat the oil in a large skillet. Add the cauliflower and salt, and sauté, stirring, until just tender
(about 8-12 minutes). Serve immediately.
If you don’t need all the cauliflower straight away, save the ‘riced’ cauliflower raw, ready for
the next meal.
Optional extra flavors and add-ins include garlic, onion, saffron, fresh parsley or other herbs,
curry spices, or peas.

Daikon and Dulse Salad
Servings: 4
• 1 lb daikon (mild Japanese radish), peeled

• 1 cup dried dulse sea vegetable, chopped (such as Eden Foods brand)
• 1/4 cup sun dried tomatoes, oil-packed, drained and diced
• Juice of 1 lime
• 2 tablespoons sesame oil
• Sea salt and freshly ground pepper, to taste
Using a course grater, grate the daikon into a med-large bowl. Add in the dulse, sun-dried
tomato and mix for a minute. Add the lime juice and sesame oil, mix well and season to taste.

SNACKS

Roasted Spiced Chickpeas
Servings: 3
• 1 can chickpeas (garbanzo beans)

• Sea salt, to taste
• 2 teaspoons of total spices- like chili powder, curry powder, garam masala, cumin,
smoked paprika, rosemary, thyme, nutmeg, cinammon or any combination you enjoy
Heat the oven to 400°F. Rinse, drain then pat dry the chickpeas. You more moisture you can get
off the better. In a mixing bowl, combine the chickpeas with olive oil and salt, then place them
in an even layer on a backing sheet. Roast for 20 to 30 minutes, stirring the chickpeas every 10
minutes. They’re done when they turn golden brown- dry and crispy on the outside, soft in the
middle. Back in your mixing bowl, toss the chickpeas with the spices, stirring to coat evenly.
They’re most crispy when they’re warm, so serve immediately for most crunch!

Pâté with Cucumber “Chips”
Servings: Makes about 2 cups

• 1 packet of organic chicken livers (about 1lb), trimmed (remove the sinew parts with
kitchen shears) and rinsed
• 1/4 cup cashews or macadamia nuts
• 1 small onion, chopped
• 2 cloves garlic, chopped
• 1 teaspoon fresh thyme (or ½ teaspoon dried)
• Salt and pepper
• Cucumbers, sliced into rounds, for serving
Heat the oil in a medium saucepan over a gentle heat. Add the chicken livers, cashews, onion,
garlic and sauté gently until cooked through, about 15-20 minutes. Add the thyme and transfer
everything to a food processor. Process until smooth and creamy, about 5 minutes (takes a little
longer to get the cashews really smooth). Add salt and pepper to taste, and process to combine
well. Transfer the mixture to a container (with lid) and store in the refrigerator. It will thicken as
it cools.
As a snack, serve 1/4 - 1/3 cup of pâté with 6-8 sliced cucumber “crackers.”

Nutty Snack Balls
Serves: Makes 3 dozen, Serving Size 2 balls
Cook Time: 20 minutes
• 3 cup mixed nuts and/or seeds (such as macadamia nuts, pumpkin seeds and
sunflower seeds)
• 1 cup unsweetened coconut, shredded
• 6 Medjool dates
• 1 lemon, zested
• 1 lemon, juiced
In a food processor, combine all ingredients and blend until a sticky dough is formed. It doesn’t
have to be completely smooth, but it does have to stick together. Keep going with the food
processor until it does. Remove the processing blade and form into 1-inch balls.
Store in an air-tight container in the refrigerator for 1-2 weeks. Can also be frozen.

Hazelnut Butter and Apple Slices
Servings: 1
• 1 apple, cored and sliced

• 2 tablespoons unsweetened hazelnut butter (may substitute almond butter)
Spread the nut butter on the apple slices and enjoy. Make a sandwich for easier portability-
spread the nut butter on one slice and top with a second slice.

Nori Chips
Servings: 4 snack-sized servings
• 5 sheets nori (a type of seaweed used for making sushi)

• Sea salt to taste
• Optional spices: garlic powder, onion powder, cayenne, miso*
Preheat oven to 350˚F. Using kitchen shears, cut the nori into squares and arrange on a baking
sheet without overlapping. Using a pastry brush, or your fingers, lightly coat the nori with oil
then sprinkle with seasoning. Flip and repeat on the other side. Bake for 15 min, then transfer to
a wire rack to cool and crisp. Will last about 4-5 days in an airtight container.

Truffle Treats
Servings: makes 16-20 balls, serving size 2 balls
Cook time 15 minutes, plus extra for soaking cashews
• 1 tablespoon coconut oil, melted

• 3/4 cup organic cocoa powder
• 2 cups cashews, soaked overnight and drained
• Pinch of sea salt
• Stevia, to taste
• 1 cup shredded dried coconut flakes
In a food processor, add the first four ingredients and blend until completely creamy. This may
take about 5 minutes, so that the cashews are completely smooth and no longer grainy. Slowly
add stevia until you reach the desired sweetness.
Remove the blade and, taking a small amount of the mixture each time, roll into small balls. Roll
each ball in the coconut flakes to coat. Keep refrigerated to harden the truffles.

SMOOTHIES & JUICES

Sea Green Smoothie
Servings: 1
• 1/2 cup cantaloupe, cubed

• 1/2 banana
• 1 handful of kale or spinach
• 1 handful of Swiss chard
• 1/4 avocado
• 2 teaspoons spirulina powder
• 1 cup water
• 3 or more ice cubes
Blend all ingredients in a high speed blender until completely smooth and enjoy!

Berry Bliss Smoothie
Servings: 1
• 1/2 cup blueberries (fresh or frozen, preferably wild)

• 1 medium carrot, roughly chopped
• 1 tablespoon ground flaxseed or chia seed
• 1 tablespoons almonds
• Water (to desired consistency)
• Ice cubes (optional, may omit if using frozen blueberries)
Blend all ingredients in a high-speed blender until smooth and creamy. Best served
immediately.

Sweet and Spicy Juice
Servings: 1
• 1 cup honeydew melons

• 3 cups spinach, rinsed
• 3 cups Swiss chard, rinsed
• 1 bunch cilantro (leaves and stems), rinsed
• 1-inch knob of ginger, rinsed, peeled and chopped
• 2-3 knobs whole turmeric root (optional), rinsed, peeled and chopped
Juice all ingredients in a high quality juicer. Best served immediately.

Ginger Greens Juice
Servings: 1
• 1 cup pineapple cubes

• 1 apples, sliced
• 3 cups kale, rinsed and roughly chopped or ripped
• 5 cups Swiss chard, rinsed and roughly chopped or ripped

Zesty Beet Juice
Servings: 1
• 1 grapefruit, peeled and sliced

• 1 apple, washed and sliced
• 1 whole beet, and leaves if you have them, washed and sliced

Protein Power Smoothie
Serving: 1
• 1 scoop protein powder

• 1 tablespoon ground flaxseed
• 1/2 banana
• 1 kiwi, peeled
• Pinch of cardamom
• Non-dairy milk or water, enough to achieve desired consistency
Blend all ingredients in a high-powered blender until completely smooth. Best served
immediately!

11 APPENDIX A: CHECKLIST FOR METHYLATION ASSESSMENT

⃣ Genetic Profiling  Ethanolamine
 AHCY  Phosphoethanolamine
 BHMT  Phenylalanine
 CBS  Tyrosine
 COMT  Creatnine
 MAO  Histamine
 MAT1A  Vanilmandilate
 MTHFR  Homovanillate
 MTR  Melatonin
 MTRR  8-OHdG
⃣ Nutrient Status (dietary intake and  Lipid peroxides
laboratory)  F2-isoprostanes
 Methionine  Neopterin/biopterin
 Cysteine ⃣ Nutrient Assimilation Capability
 Taurine  Gastric function
 DHA  Pancreatic function
 Zinc  Dysbiosis
 Magnesium  Intestinal permeability
 Potassium  Food sensitivities
 Riboflavin  Malabsorption
 Niacin ⃣ Inflammation
 Pyridoxine  Weight
 Folate  BMI
 Vitamin B12  Waist circumference
 Betaine  CRP
 Choline  Ferritin
 Sulfur  ESR
⃣ Methylation Metabolites  Dysbiosis
 Homocysteine  Small intestine bacterial
 SAMe overgrowth (SIBO)
 SAH  Periodontitis
 SAMe:SAH ratio  Comorbidity such as autoimmunity
 Cystathionine or infection
⃣ Other Methylation-Related ⃣ Oxidative Stress
 Glycine  8-OHdG
 Serine  Alpha-hydroxybutyrate
 Threonine  Pyroglutamate (5-oxoproline)
 Sarcosine  Lipid peroxides
 Phosphoserine  F2-isoprostanes

12 APPENDIX B: CHECKLIST FOR METHYLATION INTERVENTIONS

⃣ Food-Based Nutrients  Consider NAC,  NO
 Dietary planning alpha lipoic acid,  Niacin
and intake coQ10  Theophylline
assessment ⃣ Detoxification  Phenytoin
 Consider  Reduce exposure  Carbamezepine
adjustments for  www.ewg.org  Antimalarials,
methylation SNPs  Hydration pyrimethamine,
⃣ Five-R Gut Protocol  Fiber proguanil
 Remove  Organic, antibiotic-  Sulfasalazine
 Replace free, hormone-free  Triamterene
 Re-inoculate foods  Oral contraceptives
 Repair  Colorful plant foods  Cyclosporin A
 Rebalance especially deep ⃣ The Methylation Diet Food
⃣ Microbiome greens and berries Plan
 Butyrate production  Cruciferous  Foods dense in
 L. plantarum  Protein methylation
 B. bifidum  Micronutrient nutrients
 B. infantis intake  Hydration
 B. breve ⃣ Stress Management  Varied, colorful,
 B. longum  Reduce exposure whole plant foods
 B. adolescentis (high  Stress management  High fiber intake
mTHF production) techniques  Organic
 B. pseudocatenulatum ⃣ Exercise  “Low and slow”
 Prebiotics  Regular, moderate cooking
⃣ Inflammation exercise  Low carbohydrate
 Blood glucose  Personalized to (for glucose control)
management fitness/strength  Caloric restriction
 Healthy weight level  Avoid alcohol
 Resolve gut-driven  Avoid over-training  Avoid added
inflammation ⃣ Check Nutraceutical sugars
 Food allergens Interactions  Avoid antibiotics in
 Anti-inflammatory  Niacin foods
diet  Selenium  Avoid hormones in
 Stress management  Phosphatidylethano foods
 Regular moderate lamine  Avoid high
exercise  Supraphysiologic mercury fish
⃣ Oxidative Stress doses of plant  Avoid high/dry
 Diet bioactives heat food
 Exercise ⃣ Check Medication preparations
 Sleep Interactions  Avoid plastic food
 Environmental  Antacids, PPIs and beverage
toxins  Cholestyramine containers
 Infections  Colestipol  See Food Plan
 Dysbiosis  Metformin handout

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Methylation Diet and Lifestyle

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 2

from the use of information to be found in this publication.

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 3

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 4

7.10 Medication Interactions ..........................................................................................................................61

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 5

AHYC Adenosyl homocysteinase

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 6

KLF5 Kruppel-like factor 5

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 7

2 PREFACE: THE NEED FOR CONSERVATIVE YET EFFECTIVE

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 8

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 9

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 10

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 11

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 12

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 13

4.1 THE BIOCHEMISTRY OF METHYLATION

1. By the addition of a hydrogen ("reduction”) to methylene (-CH2-) groups, such as is

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 14

4.2 ENDOGENOUS METHYLATION USES

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 15

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 16

4.3 DNA METHYLATION PLASTICITY

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 17

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 18

5 THE CLINICAL PROBLEM

5.1 METHYLATION DEFICITS

It is recognized that an individual may become deficient in methylation activity in multiple

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 19

COMPETITION FOR METHYL DONORS

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 20

Frequency and effects of MTHFR polymorphisms

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 21

5.2 FOLIC ACID CONCERNS

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 22

5.3 METHYL DONOR INTOLERANCE

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 23

Case 1.0: Methyl donor intolerance with COMT polymorphism

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 24

5.4 METHYLATION GONE AWRY

UNEXPLAINED ADVERSE EFFECTS MAY BE DUE TO ABERRANT METHYLATION WHICH

IMMUNE DYSREGULATION AND DYSFUNCTION

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 25

BLOOD SUGAR DYSREGULATION

PRENATAL DEVELOPMENT DYSFUNCTION

COMORBIDITY AND MORTALITY IN DIABETIC ADULTS

© 2016 Kara Fitzgerald, ND www.drkarafitzgerald.com 26

“It’s fashionable now to use large doses of methylating agents. But in

that study of Prozac, using 15-50 mg of folic acid in depression, you

short a period as possible.

I used methylated folate to treat a woman with depression. It

happened to cure her endometriosis, too, because endometriosis, in

part, is a genetic methylation defect. So there are places for these

things, but don’t overdo it. Don’t overdo it.”

Robert Hedaya, MD, DLFAPA. Clinical Professor of Psychiatry,

Georgetown University School of Medicine. Faculty, Institute of Functional