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Autoimmune Disease 101

(Everything You Need to Know)

The prevalence of
autoimmune disease has
increased exponentially over
the last 20-30 years. It is
reported that roughly 700
million people around the
world are living with some
sort of autoimmune
“There’s no sign of this
trend slowing down;
on the contrary,
the prevalence of
diseases like type 1
diabetes, inflammatory
bowel disease, and
multiple sclerosis is
increasing at an
alarming pace. From
2001–2009 alone, the
incidence of type 1
diabetes increased by
23 percent!”
To add concern to the
growing number of
individuals living with the
condition, it appears that
conventional treatment has
little to offer in reducing the
severity and discomfort that
accompanies autoimmune
What is
The human body is
designed with a specialized
immune systemcomposed
of a complex network of
special cells and organs.
These cells and organs are
designed to defend the body
from germs and other
foreign invaders.
At the core of your immune
system is the ability to
differentiate between “self”
and “nonself”, or what is you
versus what is foreign
matter. Autoimmune
disorders, or disease,
occurs when the body’s
immune system begins
to attack and destroy
healthy body tissue by
diseases are born
when your body is
working hard to defend
itself against
something potentially
dangerous, such as an
allergen, a toxin, an
infection, or even a
food, and it fails to
differentiate between
the intruder and parts
of your own body.
Mistaking certain types
of tissues for harmful
substances, your body
turns these antibodies
against itself, wreaking
havoc on your
Autoimmune disorders
usually fall within one of
two categories: systemic or
local. Here is the difference:
 Systemic autoimmune
diseases are linked to the
production of non-specific
tissue autoantibodies,
leading to a spectrum of
damage which can affect a
wide range of tissues,
organs, and cells of the
 Localized autoimmune
diseases, on the other
hand, lead to organ-specific
conditions, affecting a
single organ or tissue.
It is important to note,
however, that the boundary
between systematic and
nonsystematic disorders can
become a bit fuzzy as the
disease runs its course. In
other words, as the effect
and scope of localized
autoimmune disorders takes
hold of the body, it is not
uncommon for the damage
to extend beyond the initially
targeted areas.

System 101
To better understand how
your body has the ability to
“attack itself”, leading to the
development of an
autoimmune disease, it
helps to know the basics
about immunology. Let’s
briefly look at the various
organs, the cells they
produce, and the role these
specialized cells play in
protecting you from illness.
Immunology basics:
 Bone marrow – found within
your bones, where immune
cells are derived.
 Thymus – A flat, pinkish-
gray gland, found in the
upper chest in front of the
heart. This is where your
T-cells pass through and
 Lymphatic system – A
critical system for the
elimination of toxic waste
from your tissues. This
system is made up of lymph
fluid, lymphatic vessels,
bone marrow, lymph nodes,
spleen and tonsils.
 T-cells – These immune
system cells function like
“warriors” and mature in the
thymus. Once mature t-
cells enable each individual
T-cell to recognize only one
of millions of antigens, at
which time they migrate into
your lymphatic system and
circulate in the blood.
 B-cells – These immune
cells are produced in and
by your bone marrow and
are responsible for the
secretion of antibodies.
You’ll notice the term “t-
cells” used multiple times in
the above list, and as you
may have already gathered
T-cells are of great
importance. (#) These cells
are taught to recognize
invading cells, or non-self
cells, from your own cells.
Remember, a normal
functioning immune system
only attacks substances and
infections that are thought of
as foreign invaders, such as
cancer cells. When the
immune system is
“confused”, it begins to
attack healthy cells found
within the body.

Target Organs
and Tissues
The triggers for autoimmune
disorders are rather
variable, and may be
brought on by the following
 Environmental exposure to
chemical solvents
 A drug response
 Contraction of a viral or
bacterial infection
 Sunlight or radiation

Just as the triggers for an

autoimmune reaction are
varied, the debilitating effect
vary as well depending on
the target organs and
tissues affected by
disorders. (1) With more
than 80 types of
autoimmune disorders,
some common tissue types
and bodily sites that the
immune system can begin to
attack include:
 blood vessels
 connective tissue
 endocrine glands (i.e.
thyroid or pancreas)
 joints
 muscles
 red blood cells, and
 skin

Keep in mind it is possible to

have multiple tissues and
organs attacked by the
immune system, resulting in
the diagnosis and presence
of more than one
autoimmune condition at the
same time.

Signs and
Symptoms of
There is some amount of
mystery and confusion
behind certain autoimmune
conditions, such as multiple
sclerosis, rheumatoid
arthritis and thyroiditis. (2)
Part of what contributes to
the unknown lies in the fact
that the biological basis, and
some of the most common
symptoms that accompany
such debilitating
illnesses, may not be linked
to one specific infection.
“Despite its
prevalence, the level
of basic autoimmune
research funding is
below 3% of the
National Institutes of
Health (NIH) total
budget, which may
explain why we
understand so little
about the roots of
these diseases.
Indeed, AARDA
reports that the whole
arena of autoimmune
research is in its
infancy…We do know
there are factors at the
root of autoimmune
development, which
include both genetic
and environmental
While the biological or
genetic and environmental
factors contributing to the
development of an
autoimmune disorder may
not be well understood,
there are some well
documented signs and
Experiencing any of the
symptoms listed below may
indicate the presence of an
autoimmune disease;
however, experiencing more
than one of these symptoms
could increase the likelihood
of an autoimmune disorder:
 Joint pain or muscle pain,
accompanied by weakness
or tremors
 Unintentional weight loss or
weight gain
 Insomnia
 Intolerance to heat or cold
 Rapid heartbeat
 Recurrent rashes or hives
or sun-sensitivity
 Brain fog, difficulty
concentrating or focusing
 Abdominal pain, bloody
stools, diarrhea
 White patches or ulcers in
and around your mouth
 Dry eyes, mouth, or skin
 Numbness or tingling in
hands or feet
 Multiple miscarriages or
blood clots
It is estimated that up to 1/3
of the risk factors for
developing an autoimmune
stem from heredity and
genetics; however, gender
plays a very large part in the
development of autoimmune
disease. (3)
Interestingly enough, the
female population accounts
for about 75% of Americans
afflicted by autoimmune
conditions. (4) On top of
that, autoimmune disease
constitutes some of the
leading causes of death and
disability in women, up to
the age of 65.
Though the relationship
between sex and the
prevalence of autoimmune
disease is not well
understood, researchers
have been able to document
that women have higher
levels of antibodies,
mounting larger
inflammatory responses
than men when their
immune systems are
As hormones fluctuate,
autoimmune diseases
responds in accordance to
such shifts. (5) When a
women becomes pregnant,
has her menstrual cycle,
goes through menopause,
or takes birth control, the
severity of the condition may
change. (6) Despite the
large percentage of the
female population at risk of
developing an autoimmune
disorder, autoimmunity is
not often discussed as a
potential health issue.

Thyroid disease, lupus,
multiple sclerosis, and
rheumatoid arthritis top the
list as some of the most
commonly diagnoses
autoimmune diseases in the
United States. Let’s take a
closer look at these
commonly diagnosed
conditions so you have a
better understanding of how
autoimmune disorders can
impact your health.
Thyroid Disease: Graves’
disease and Hashimoto’s
disease are the two types of
autoimmune diseases that
target the thyroid. Graves’
disease leads to an
overactive thyroid
(hyperthyroidism), whereas
Hashimoto’s disease causes
an underactive thyroid
(hypothyroidism). Most
individuals are diagnosed
with thyroid disease
between the age of 20 and
30 years old, and women
have higher rates of thyroid
disease compared to men.
The thyroid gland is the
main metabolic regulator of
the body, thus any sort of
gland dysfunction affects
your metabolism. In the
presence of Graves’
disease, as the thyroid gland
is attacked by the body’s
antibodies, inflammation and
swelling result. This in turn
leads to hyperthyroidism, or
an overactive metabolic
state, whereby the body
basically goes into
overdrive. As the metabolic
rate increases, one may
also experience an increase
in heart rate and blood
Hashimoto’s thyroiditis is
caused by antibodies
reacting against proteins on
the thyroid; however, this
disease is characterized by
a gradual destruction of the
gland itself. As the gland is
destroyed, the body is no
longer able to produce
critical thyroid hormones
required by the body, and
metabolic rate will decrease,
most often leading to
unintentional weight gain.
Systemic Lupus
Erythematosus (SLE): SLE
(i.e. “lupus), is a chronic,
autoimmune disorder that
affects many organs and
tissues, most often skin,
blood, joints, kidneys, lungs,
and the heart. Antibodies
produced in response to the
disorder lead to
the formation of immune cell
complexes, which build up
over time various tissues
leading to pain,
inflammation, or destruction
of the areas of the body that
are under attack.
For many,
lupus is considered a mild
condition and will only affect
a few organs. For others,
however, it can trigger
serious and potentially life-
threatening, conditions.
Lupus can occur at any
age, and the disease is 10-
15 times more common in
women than men.
Studies have shown that
some lupus patients have
low levels of
DHEA (i.e. dehydroepiandro
sterone), and further studies
are continuing to investigate
the contribution of this
hormone to the onset of the
Sclerosis (MS): Multiple
sclerosis is a chronic
inflammatory autoimmune
disease, that specifically
targets the central nervous
system, thus impacting
normal function of the brain
and spinal cord.
In MS, the body produces
excess antibodies that go on
to specifically attack the
myelin, which is a protective
sheath that covers nerves.
As a result of the attack,
neurological, cognitive, and
psychological problems set
in. One may experience
weakness or paralysis of
limbs, numbness, vision
problems, speech
difficulties, problems with
walking or changes to motor
skills, and sexual
MS is actually the most
commonly diagnosed
neurological disease in
young adults and, most
often detected in between
the age 20 and 40. MS, like
many other conditions, is
much more prevalent
(almost twice as much) in
women compared to men.
Arthritis (RA): Rheumatoid
Arthritis is a widespread,
disabling autoimmune
disease, affecting the joints
and muscles of the body.
The most frequently
impacted joints are those
that are free-moving,
including small joints of the
hands, knees, ankles, hips,
elbows, wrists and
RA results after the body
launches an autoimmune
attack on the synovial
membranes, the tissue that
lines and cushions your
joints. In response to the
attack, one may experience
inflammation and pain. As
the condition continues to
progress, the pain and
swelling increase, and over
time this may result in
destruction and deformity of
the bones.
RA typically surfaces
between the age of 25 and
50, though the symptoms
may be mistaken as a
normal part of aging. The
condition afflicts females two
to four times more than
males. Unfortunately, RA is
rather progressive, despite
treatment protcols. Many
times the objective of
treatment is quite simply to
control inflammation,
prevent or slow joint
damage, hopefully leading
the condition into remission.
To date, there is no cure for
the majority of diagnosed
autoimmune disorders, thus
individuals are faced with a
lifetime of debilitating
symptoms, which may
include loss of organ or
tissue function, and
extensive medical costs.
The goal of treatment is
most often targeted at the
reduction chronic symptoms,
decreasing the intensity of
the immune system activity,
and being able to maintain
the immune system’s
“normal” ability to fight
foreign invaders.
Treatments vary widely and
depend on the specific
disease and the symptoms.
Take for example an
individual living with Type I
Diabetes, where the target is
to replenish insulin levels,
usually through injections or
supplement the body with a
hormone or vitamin that the
body is lacking. This is
much different than the
treatment of an autoimmune
disorder that either directly
or indirectly affects the blood
or the circulatory system
(i.e. autoimmune hemolytic
anemia, lupus, or
antiphospholipidal antibody
syndrome.) Treatment of
these conditions may
require blood transfusions.
In the case of an
autoimmune disorder that
affects the bones, joints, or
muscle (i.e. multiple
sclerosis or rheumatoid
arthritis), treatment may be
geared towards the
maintenance of mobility or
the incorporation of a
medication to suppress pain
and reduce inflammation.
It is also not uncommon for
medicine to be prescribed
as way to control or reduce
the immune system’s
response. Popular
medications include
corticosteroids and
immunosuppressant drugs
(i.e. azathioprine,
mycophenolate, and

Keeping Your
Keeping the immune system
healthy and functioning
appropriately involves taking
care of your health on many
different levels. Most books
on the topics, as well as
many health experts,
promote the simple concept
of “living well”.
Whole body wellness
involves basic, common
sense practices like
following a healthy diet,
getting enough rest or
exercising consistently, drink
ing alcohol only in
moderation, and avoiding
To take your wellness to the
next level, there are
some additional steps you
can take to keep your
immune system healthy
such as:
 Avoiding all possible
exposure to environmental
toxins such as mercury,
poisons and heavy metals.
 Avoidance of taking
unnecessary drugs.
 Choosing your foods wisely
with an understanding that
your diet plays a large part
in healthy functioning
immune system.
 Regular sexual activity has
been found to be beneficial
through its contribution to a
healthy hormone balance.

Now that you have a better
understanding of
autoimmune disease and
how it can impact your
health, you may be asking
yourself, “Do I need to follow
a Paleo gluten-free diet to
help boost my immune
system? What about
alternative supplements or
more holistic treatments?”
If you are asking yourself
these questions, join the
club! Of the estimated 23
million people in the United
States suffering from
autoimmune disease, most
are asking themselves these
same questions daily,
hoping for a safe solution
without medical and drug-
related intervention.
If you suffer from an
autoimmune condition, or
you know of a loved one or
friend who may be
struggling with the condition,
you may already be aware
of the Autoimmune Paleo
diet (AIP). Many individuals
are transitioning to a refined
paleo eating plan in an effort
to improve life-disrupting
symptoms including pain
and fatigue.
While medical experts have
offered mixed feedback as
to how effective the Paleo
diet is in treating
autoimmune disease,
individuals who have a
vested interest in following
the dietary plan consistently
support the AIP, claiming
that it has improved their
quality of life.
While the AIP may be
initiated as a way to manage
an autoimmune issue,
chances are those suffering
from autoimmune disease
also have a poorly
functioning digestive tract. If
the gut is not in good shape,
byproducts of all of the
things passing through the
intestines are leaking
through the gut barrier and
into the blood stream,
stimulating the immune
system to respond with
greater intensity.
The AIP is designed to help
decrease inflammation and
immune system stimulation
at the same time.

The Standard
Diet Versus
Paleo Diet
Many standard versions of
the Paleo diet suggest
starting with a strict
elimination phase, meaning
that the following foods
should be completely
 grains
 legumes
 dairy
 refined sugars
 modern vegetable oils
 dairy, and
 processed food chemicals,
including gluten.
“The Autoimmune
Protocol (AIP) diet
works to reduce
inflammation in the
intestines. Many
elimination diets are
not complete enough
and often do not
remove immune
triggers that promote
inflammation in the
gut. AIP works to calm
inflammation in the gut
and also calm
inflammation in the
body. And while
autoimmune disease
can never be cured, it
can be put into
When following the AIP, the
basic Paleo dietary
recommendations do not
change; however, the
protocol and dietary strategy
is a more strict version. As
part of the autoimmune
protocol, most advocates
and Paleo experts would
recommend that you also
 eggs (especially egg
 nuts
 seeds (including cocoa,
coffee, and seed-based
 nightshades (including
potatoes, eggplant, sweet
and hot peppers)
 alcohol
 artificial sweeteners
If you want to read more
about nightshades and why
they may be best to avoid as
part of the AIP, here is
a great resource!
While the AIP is a bit more
rigid than the standard
Paleo diet, it is definitely a
more natural, holistic
alternative to the traditional
medications and treatments
that over time can feel more
invasive or cause a whole
host of undesirable side
For more information on the
AIP, including a list of great
tasting recipes to
incorporate, check out this
While you should try to get
in the bulk of your vitamins
and minerals through your
diet, there are some
supplements with promising
potential in reducing one’s
risk of the development of
autoimmune disease or as
an adjunct to your treatment
plan. If you are already
being treated for an
autoimmune condition, be
sure to check with your
medical provider before
adding in any supplements
to your diet.
Here are three supplements
that are gaining attention
and traction with respect to
their autoimmune benefits:
Vitamin D: One of the most
intriguing areas of nutritional
research involves vitamin D.
For decades, science has
been able to correlate a
positive relationship
between sunlight exposure,
vitamin D levels, and
autoimmune disease risk.

For example, there have

been studies conducted
specifically related to
multiple sclerosis indicating
that those living with the
disease have lower levels of
vitamin D than comparison
groups. Interestingly
enough, many autoimmune
diseases, namely multiple
sclerosis, type I diabetes,
and lupus become more
common the further away
one lives from the equator.
One particular study,
following subjects for 30
years, revealed that children
born in Finland in 1966 who
received supplemental
vitamin D during the first
year of life had a
significantly lower risk for
developing type 1 diabetes.
On the other hand, children
with vitamin D deficiency
during the first year of life
had a significantly higher
risk for developing type 1
diabetes. (7)
Another study investigating
vitamin D’s impact on
rheumatoid arthritis, known
as the The Iowa Women’s
Health Study, correlated a
reduced risk of RA
development as vitamin D
intake increased. (8) Yet
another study, known as
The Nurse’s Health Study,
found a positive, protective
relationship between vitamin
D supplements and multiple
sclerosis risk. (9)
Finally, a more recent
study analyzing data from
participants enrolled in the
Multiple Sclerosis
Surveillance Registry
suggests that exposure to
vitamin D before multiple
sclerosis onset may help to
slow disease-related
neurodegeneration, thus
causing a delay in MS
progression to disability.
Why is vitamin D work so
potentially beneficial to your
immune system? In the
1970s, scientists
discovered vitamin D
receptors in many of the
body’s cells (i.e. islet cells of
the pancreas, lymphocytes,
and colon enterocytes).
Upon the discovery of the
cells, further information was
gathered revealing vitamin
D’s ability to help keep the
immune system functioning
properly through the
inhibition of the proliferation
of T cells and further
reduction in the production
of proinflammatory
Although there seems to be
suggestive evidence of the
benefits of vitamin D on the
development of autoimmune
disease, there is still much
to learn. Clinical studies
have not thoroughly
investigated the benefit to
giving large doses of vitamin
D in those at risk or battling
autoimmune disease. In
addition, the level of vitamin
D required to prevent
disease and maintain health
may not be the same for
every individual.
Prebiotics and Probiotics:
Researchers with a
particular interest in
autoimmune disorders have
begun to question the
impact of balancing the gut
microbiota on the
development of autoimmune
disease. It appears that
disruption of the intestinal
ecosystem equilibrium can
be traced to many disease
states, including
autoimmune disorders.

Prebiotics and probiotics

may be a beneficial and safe
therapeutic intervention for
those dealing with
autoimmune disease, as
studies conducted within
animals and humans have
positively correlated the
presence of probiotic
cultures to enhanced
activity of immunoreactive
cells, thus regulating anti-
inflammatory responses.
For this very reason,
researchers are exploring
how the gut microbiome
may be different in children
with type 1 diabetes versus
children without the disease.
(10) Other studies are
linking an improvement in
pain levels and self-
assessed disability in adults
living with rheumatoid
arthritis.(11) On top of
that, preliminary
studies have suggested
that probiotics may be of
benefit for those living with
colitis and inflammatory
bowel disease because they
may balance the gut
microflora leading to a
stronger intestinal defense
Just as stated in relation to
the topic of vitamin D, the
correlation between
probiotics and autoimmunity
is still in its preliminary
phases. If this is an area of
interest to you, look for
future studies conducted in
this area to help answer
some of the unknown
answers to some important
Omega-3 Fatty-acids: It
appears that omega-3 fatty
acids can lead to promising
benefits and improvements
in the risk factors and
treatment of autoimmune
disease, particularly with
those found in fish oil (i.e.
EPA and DHA). According
to a 2002 review of fish oil
benefits, omega-3 fatty
acids posses potent
components, which might
make them rather useful in
the management of
autoimmune diseases.
Omega-3 fatty acids have
been studied in the following
autoimmune conditions:
 Arthritis
 Crohn’s disease
 Lupus
 Multiple sclerosis, and
 Rheumatoid arthritis
Researchers conducting
studies out of Australia
following subjects suffering
from rheumatoid arthritis
generated data supporting a
reduction in joint tenderness
and decreased use of
nonsteroidal anti-
inflammatory drugs with fish
oil supplementation. (12)
Additional studies have
shown that subjects
experience improvements in
time to fatigue and grip
strength with an increase in
fish oil consumption. (13)
For those suffering from
systemic lupus, placebo-
controlled trials indicated
that omega-3 fish oils
improved symptomatic
disease activity. (14)
Look for further research on
how omega-3 fatty acids
may help to treat
autoimmune disorders, and
if you are interested in
incorporating a fish oil
supplement for other
reasons, check with your
medical provider before
adding supplementation into
your diet.

Bottom Line
When your body’s immune
system is functioning just as
it should, it is able to sustain
a marvelous defense
system, protecting your
body against foreign
invaders and inflammation
through complex
communication systems
involving your cells, tissues
and organs. A healthy
immune system involves
clear communication within
the body, where it is able to
tell the difference between a
foreigner and itself;
however, when the immune
response is not functioning
properly causing the
communication system to
breakdown, the immune
response is flawed.
Autoimmune disorders
develop and progress as
your body’s immune system
begins to attack and destroy
healthy body tissue by
mistake. Over time the body
cannot properly regulate the
intensity of the immune
response causing symptoms
to surface, some of which
can be debilitating and
painful. Symptoms
associated with autoimmune
disease are wide and varied,
but may impact multiple
biochemical processes
causing dysfunction with
your circulatory system,
digestive system, endocrine
system, urinary system,
lymphatic system,
respiratory system, nervous
system and reproductive
Traditional treatment
is targeted at the reduction
chronic symptoms,
decreasing the intensity of
the immune system activity,
and being able to maintain
the immune system’s
“normal” ability to fight
foreign invaders. Non-
traditional treatments that
are gaining greater
popularity involve lifestyle
and dietary modifications,
and in the future may
incorporate particular
supplementation protocols
involving the use of vitamin
D, prebiotics or probiotics,
and omega-3 fatty acids.
As for dietary intervention,
though there is some debate
around the Autoimmune
Paleo Protocol (i.e. AIP), it
may be a safe and helpful
dietary strategy for those
who have tried just about
every other treatment plan.
If you need a bit more
incentive to follow the AIP
protocol given how rigid it
may be, perhaps reading the
following following
resource will be a helpful

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Ask a Question

1. Susan

April 5, 2016 at 10:17 pm

I found this article really interesting. I have some odd persistent problems that doctors have
had no success with. The most annoying one is my skin. I have redness across my nose and
cheeks and between my brows. Sometimes its accompanied by little pimples. I also have a
chronic problem with me right ear which is always itchy and sore and wet after scratching. I
am quite certain its diet related. I’m otherwise quite well but always vague and agitated and
tired. I would like to address this through diet and lifestyle but its so challenging to make
these changes. It feels like a lot of effort. Do you have any advice about how to get started?

2. Joy

April 6, 2016 at 7:52 am

I have had RA diagnosed in 2011. Its now 2016 and I’m into my 4th year of paleo. I am well
have been weened off the strong meds. I take vit D + a probiotic. I have had no flare-ups for a
long time.


3. Linda Polan

April 7, 2016 at 2:23 pm

This is a very thoughtful and informative article. I wish there was mention of functional
medicine practitioners, their role in modern medicine and how they treat the root cause of
autoimmune disease and chronic illness.