Functional Genomics
Dr. Deanna Cherrone • April 8, 2025
Functional genomics refers to how the information contained in our DNA is read and acted upon. Evaluating how each person’s unique genome functions can allow us to understand symptoms and disease processes, and personalize care accordingly. The study of functional genomics is evolving rapidly. Environmental and lifestyle factors such as sunlight exposure, the air we breathe, the water we drink, the food we eat, the chemicals we are exposed to in personal care products, cleaning products and even some working environments, can all affect genetic expression along with a whole host of other factors.
During conception when the sperm and egg come together, half the genetic code from each parent is passed down to the child in the form of chromosomes. Each chromosome carries hundreds to thousands of genes. Genes code for proteins and enzymes that allow us to take food, water, oxygen and sunlight to run all of the biochemical reactions that allow our bodies to function. When these reactions are disrupted or dys-regulated, symptoms and disease can result.
We know that humans are 99.9% genetically identical to each other, so how significant is that 0.1% difference when it comes to health? The more we learn about the human genome, the more we realize that it can make quite a difference with regard to disease susceptibility. An extreme example of this that we are all familiar with is trisomy 21, more commonly known as Down’s Syndrome, where an extra copy of chromosome 21 is inserted into the genome. These individuals are often born with characteristic facial features, developmental delays, congenital heart defects and other abnormalities.
Genetic variation refers to changes in DNA sequencing. These variants can cause a gene to be more active, less active, or to have no real significant effect at all. Another important factor is whether that variant is homozygous or heterozygous. Homozygous refers to both parents donating the variated gene while heterozygous variants result when one parent passes on the genetic variant. Heterozygous gene activity can be 70 to 80 percent of normal (wild type), whereas homozygous variants can have as little as 30 percent activity. There are exceptions to this such as when there is an up-regulation or “gain of function” variant where the activity of the gene is increased beyond what is considered “normal.’
Genetic variants can also explain why some people have symptoms and disease, while others do not. For example, the ABP1 and HNMT genes create enzymes that break down a chemical in our body called histamine. Histamine is released by the immune system in response to foreign toxins, pathogens and/or allergens. Exposure to mold, extremes of temperature, Lyme disease, the Lyme co-infections, pesticides and plastics can all trigger histamine release. Also, eating certain foods such as bananas, avocados, fermented and packaged/processed foods which contain high amounts of histamine can sometimes be problematic for those with these genetic variants. If we are unable to break down histamine efficiently it sets us up for excess inflammation which we know contributes to ill health and disease. High histamine is implicated in allergies, anxiety, insomnia, headaches, migraines, brain fog, skin rashes, dizziness, IBS, diarrhea, constipation, nausea, bloating and painful menstrual periods. Knowledge of a genetic susceptibility to high histamine allows for the opportunity to be more intentional with dietary and lifestyle choices, as well as supplementation with specific nutrients, to help the body better break down histamine.
Another gene that has the potential for impact on one's day-to-day life is the CYP1A2 gene. This gene is responsible for greater than 95% of the metabolism of caffeine. Variations in this gene offer an explanation as to why some people tolerate caffeine better than others. Individuals with certain homozygous variants metabolize caffeine much slower. It has been hypothesized that the half-life (the time it takes for half of the substance to be eliminated from the body) of caffeine in these individuals can be up to 9.5 hours! This could explain why some people can’t sleep even though their last cup of coffee was at 10:00 AM. Half of the caffeine they ingested is still in their system at 8 pm…
The interplay between lifestyle, environment and genes is called epigenetics. Epigenetics affects the way genes are expressed WITHOUT changing DNA sequencing. Epigenetic factors include things like sleep, stress, exercise/movement, diet, exposure to pathogens and toxins, as well as drugs, supplements and over the counter medications. Many claim that stress is worse than smoking a pack of cigarettes per day when it comes to health so it is essential that we all develop stress management strategies to mitigate this factor. Many human diseases such as cancer, neurodegenerative diseases, autoimmune illness and some psychiatric/mental disorders can be triggered by some of the choices we make in how we choose to live our lives. Genes provide POTENTIAL for disease but they are NOT our destiny. The environment in which our genes “live” determines whether a gene gets turned on or stays off. With this information we realize that we have a lot more control over our health based on the daily lifestyle choices that we make.
Immune health has been all the rage lately, and rightfully so. With the Coronavirus circulating it is more important than ever to keep yourself healthy and strong. Having a healthy, robust immune system can prevent you from getting sick at all or ending up in the hospital if you do happen to get infected. There are many interventions that can help immune function. Some are well known like taking Vitamin C. I am going to focus on some that are completely free. That’s right, you don’t even need Amazon to have access to these remedies. 1. Mindfulness Meditation: Studies show that after an eight week meditation trial period participants had lower Nf-Kappa Beta (NFKB) levels. For those of you who haven’t been following the biochemistry of disease, having high levels of this stuff is bad and low levels is good. The fact that these participants showed reductions in NFKB means that their immune systems were working more effectively. If you are new to starting a meditation practice I would recommend trying an app; Calm, Headspace and 10% Happier are all great FREE options (See, still no Amazon necessary). For those who don’t want to use an app, you can start by finding a comfortable place to sit where you can rest your back and head. Keeping your head up is important because you want to stay awake during your meditation. Once you are comfortable, start to focus on your breath, let it flow in and out of your lungs as naturally as possible. The first few times you do it, it will feel more forced than natural but that is OK. As you focus on your breath, notice if thoughts start to come up. Thoughts will appear and if they don’t on your first try at meditation, you should quit your job and become a monk. The key to mindfulness is noticing that you have started to think (about food, sex, work, your favorite TV show) and keep bringing your attention back to your breath. That is the essence of mindfulness. You are supposed to think, it is like doing bicep curls for your brain. Each time you bring your thoughts back to your breath, that is a rep. 2. Sleep: It is well established that sleep is a major factor in supporting a healthy immune system. Did you know how important light is in getting good quality sleep? The answer: Very important. Light regulates your circadian rhythm which basically tells you when you should wake up and when you should go to sleep. Your immune system functions in this same way. If you don’t sleep, the natural rhythms of your immune system can become disrupted. Light modulates all of this. Getting exposure to good quality light in the morning and avoiding bad light a few hours before bed can help you sleep better and help your immune system stay more balanced. “Bad” light is the highly concentrated blue light that comes from your phones, computer and TV screens, and even LED lights. This kind of light tells your body that it is time to be awake which throws your circadian rhythm off. The most important thing you can do to address this is to get sunlight as soon as possible after waking. Actually, you don’t even need sunlight, just light from outside will do. So, first thing in the morning, open up your window and let some of that natural light in. Even better, you can go outside (I know, crazy right). The simplest way to eliminate blue light exposure at night is to turn off all your screens a few hours before bed time. For people who need to work or who like to watch TV at night there are a few options. An app called f.lux modulates your computer’s light making it darker and warmer so you are being exposed to less blue light. If you want to go the extra mile there is a company called TrueDark that makes red tinted glasses. These glasses block out all of the blue light and other junk light allowing you to use screens later without the strain it causes. You can get these directly from the True Dark website. 3. Food: I could call this section Eat Your Veggies because that is the simplest way to put it. In the interest of giving complete information, let’s go even further. You should avoid gluten, dairy, soy and processed food like the plague. These are pro-inflammatory foods and unless you are eating 100% organic the pesticides Four Easy Ways To Build A Healthy Immune System they come with add even more fuel to the fire of inflammation. These foods cause reactions in the body similar to that of a foreign invader. And who has to deal with that reaction? You guessed it, your immune system. The more taxed your immune system is from dealing with what you eat, the less resources it has to fight off real invaders like viruses and bacteria. I want to focus on gluten because it can cause the release of a protein called zonulin which regulates the amount of space between the cells lining the gut. When there is excess zonulin these cells pull apart causing a leaky gut. A leaky gut allows proteins from your food to get into the bloodstream. Large food proteins do not belong in the bloodstream so when the immune system sees them there it treats them as it would a foreign invader. This reaction can trigger the body to go into attack mode and begin to attack itself. An extreme oversimplification, but this is the basis for developing autoimmune disease. Having an autoimmune disease where the immune system is already working overtime can potentially lead to complications from any viral exposure. Having a healthy gut is extremely important because 70% of the immune system is housed in your gut. The type of food you eat can determine the health, or lack thereof in your gut. When you eat, you are not only feeding yourself, you are building your immune system. If you build your immune system with high quality veggies, healthy fats and clean lean proteins, you will build a strong immune system. If you are feeding your gut with processed foods, sugar, gluten, dairy, and soy, it will likely become dysfunctional and lead to poor immune health limiting your ability to fight infection. 4. Exercise: Light to moderate exercise is another way to boost your immune system. Hormesis is the main point of exercise. It is a small controlled stressor that makes us grow stronger and build endurance and resilience. Taking a walk in the forest has been shown to increase natural killer (NK) cell levels in the bloodstream. NK cells are important immune cells involved in killing viruses. Another important benefit of exercise is its ability to stimulate nitric oxide production. Nitric oxide (NO) dilates blood vessels, increasing blood flow which is very important when we are trying to fight infection. We want those immune cells to get to the site of infection as quickly and efficiently as possible. NO also plays a huge role in cardiovascular health which we know is an important predictor of susceptibility to the Coronavirus. While the theory that prolonged intense exercise leads to infection has been proven faulty, the immune system does take longer to recover and strengthen with the stress of high intensity exercise. If you have trouble sleeping stick to light exercise so as to not stress an already stressed immune system. The lymph system is our body’s “waste tract” where all the things we don’t need get moved through and out of the body. Walking is the most effective way to increase and stimulate lymph flow in the body. Other types of gentle exercise to consider are: Yoga, Tai Chi, Qi Gong, and stretching. With these four strategies, you can improve your immune health with minimal to no cost at all. Implementing one strategy can also help with the others. For example, when you exercise you are likely to sleep better. If you focus on eating healthy, you may have more energy to exercise. All of the body systems are connected, improve one and you improve the others. Stay safe, healthy, and strong! Jacob Appleton, INHC - Integrative Nutrition Health Coach Resources : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940234/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256323/#Sec7title https://medlineplus.gov/ency/article/007165.htm Four Easy Ways To Build A Healthy Immune System (cont.)
We are spending more and more time indoors these days and we have come to learn that the indoor air we are breathing in is very unhealthy. Volatile Organic Compounds (VOCs) such as formaldehyde from buildin materials, the off gassing of furniture, paints, rugs, personal care and cleaning products, gasoline from an attached garage, pesticides used in and around the home, improper venting of appliances and exhaust/bathroom fans to the outside, even cooking and toxins from mold and bacteria can create these unhealthy compounds which we are breathing in. Making sure that we have adequate air filtration in our homes and workplaces is a very important part of staying or becoming healthy. We are encouraged to drink more water as a way to improve our health but is that water free of impurities? There are many contaminants in our water today that we do not want to be putting in our bodies. These include chemicals, bleach, heavy metals like lead, pesticides, micro-plastics from plastic water bottles, glyphosate from round up, bacteria, viruses, protozoa, parasites and the toxins produced by these micro-organisms as well as many medications. Having adequate water filtration to make sure that we are not ingesting these toxins is also another piece of the puzzle of maintaining and/or achieving health. Ideally want to be drinking out of glass or stainless steel NOT plastic! Sunshine gets a bad rap! We lived outside for millennia and were not plagued with skin cancer. Could it actually be all of the chemical sunscreens that we lather on our bodies that are contributing to the increase in skin cancers we are seeing? We also know that many people suffer with seasonal affective disorder when they do not get enough exposure to light so sunlight can definitely help with mood and mental health. There is also a study showing that sunlight can reduce blood pressure by increasing levels of nitric oxide which helps blood vessels to dilate improving circulation and heart health. Sunlight is also what allows for the production of vitamin D which has so many health benefits in the body. Bone health, immune health and blood sugar regulation are just a few of the perks of the sunshine vitamin D! So…if you can’t get outside then make sure to take vitamin D. REAL food that comes directly from nature is one of the best medicines. I think we can safely say that the Standard American Diet (SAD) is not providing us with the nutrients that we need to keep disease at bay. 87% of Americans are metabolically unhealthy! These processed manmade foods are laden with refined sugar, flour, salt and unhealthy fats. We definitely cannot outsmart mother nature by making foods in a plant or a lab and expecting them to provide what we need for optimal health. We want to be eating mostly plants with some healthy animal protein sources grass fed beef, lamb and bison, pasture raised poultry and pork and wild caught fish. Limit large fish which are more likely to have higher levels of mercury in them. Eat organic as much as possible to reduce exposure to pesticides/chemicals. Look for Paleo or Keto recipes online to replace favorite recipes. I also like Mark Hyman’s new book The Pegan Diet = a combination of paleo and vegan - the best of both worlds - lots of plants with clean, healthy animal protein sources. Movement is essential for all of us. We are not meant to be sedentary beings but for some who are struggling with more energy depleting illnesses their ability to do exercise may be limited. Therefore, the “no one size fits all” is important even when we talk about exercise. It is important to listen to our bodies. Getting exhausted or ill after a certain amount of exercise tells us that we are overdoing it and need to cut back on the amount of time spent doing the exercise and/or the intensity of the exercise. It is also important to get a mix of cardio, strength training and stretching in our daily exercise routine. I tell my patients to schedule exercise into their day every day. Put it in your calendar! It might be 5 minutes or 50 minutes but every little bit counts. Exercise can help control weight and blood sugar, reduce risk of heart disease and Alzheimers, improve mental health and mood and help us to manage stress in a better way. Deep restorative sleep for 7-10 hours per night is essential. This means sleeping through the night and waking up in the morning feeling refreshed and rested. Getting natural light into our eyes as soon as possible after waking is a great way to reset our circadian rhythm to get more sleep. Natural light directly affects the pineal gland to produce more melatonin which affects sleep quality. It also increases the production of serotonin which can reduce stress and improve mood. Keeping your room completely dark and cool - 68 degrees - while you sleep is another way to help you get a good night sleep. Stress is here to stay so we need to learn how to mange it. Each of us has different ways that we relax. For some it might be exercise, reading a good book, taking a walk in nature, doing deep breathing exercises, yoga, meditation, knitting, fishing or even washing the dishes. The list is endless which is great news. All it requires is that whatever we choose to do we do it mindfully, with full attention and focus on what we are doing. When we do this we get out of the mental chatter in our heads and into our bodies lowering the stress response and increasing the relaxation response in the body. Personally, I start my day with a gratitude meditation in which I go through a list of all the things that I am grateful for in my life. It is a great way to start the day and it reminds me of what is most important in my life. Laughter is a great way to lower stress so find ways to bring more of this into your life. Healthy Resources: For air and water filtration systems to meet your specific needs please contact Wright Way Environmental Technologies at 586-677-1650 for a free consultation. https://pureairpurewater.com/ The sunshine vitamin - take D3 with K2 - doses for optimal levels are in the 2000-10,000 IU range per day depending on the person. For the best chicken and lamb - Circle C Farm - https://www.circlecfarmfl.com/ For the best beef and lamb - Aldersprings Ranch - https://www.alderspring.com/ For the best bison - Wild Idea Buffalo - https://wildideabuffalo.com/ For the best wild caught fish - Vital Choice - https://vitalchoice.com/ Thrive Market is a good place to shop online for Paleo and Keto items if you must eat processed foods. https://thrivemarket.com/ Helpful food lists: https://mastcell360.com/low-histamine-foods-list/ https://gundrymd.com/dr-gundry-diet-food-list/ Peloton - has a great monthly subscription for yoga, pilates, strength training etc. that you can do at home even if you don’t have a bike. https://www.onepeloton.com/bike True Dark glasses to keep out junk light from overhead and lighting and lamps, computers, TVs, and other electronic devices. https://truedark.com/ Sleep Cycle app - to monitor your sleep patterns Sleep sounds app - to help you fall asleep Calm - a magnesium powder that can help you get to sleep For stress management: DNRS = Dynamic Neural Retraining System - https://retrainingthebrain.com/ The Gupta Program - https://www.guptaprogram.com/ The Emotion Code is a book and they do have practitioners who can guide you through the process if you would like - https://discoverhealing.com/ Brain Tap - https://braintap.com/healing-with-sound/ Safe and Sound - https://integratedlistening.com/ HemiSync - https://hemi-sync.com/ Vagal Nerve Exercises https://www.arcvic.org.au/34-resources/402-vagus-nerve-exercises Wishing you the best in health! Dr. C
Vector borne illnesses are diseases caused by infectious pathogens such as bacteria, viruses, parasites and protozoa that are transmitted to humans through the bite of an infected vector. Common vectors include mosquitoes, ticks, fleas, lice, bedbugs, sandflies and black flies. Mosquitoes are the most common vector and transmit malaria and other illnesses such as Zika virus, Yellow fever, Dengue fever and West Nile virus. Lyme disease is the most common vector borne illness transmitted by ticks in the United States and will be the focus of this discussion. The CDC estimates that there are more than 300,000 cases of Lyme disease diagnosed each year. The expansion of animal reservoirs is one of many reasons for the increasing rates of tick borne illness (TBI). International travel has increased the risk because ticks can be transported by both people and pets. Also, greater awareness of the disease and better diagnostic tools are responsible for the uptick in diagnosis. For ticks to thrive in nature, they need to have an animal reservoir - a mammal that can harbor the pathogen. On the U.S. east coast, deer and white-footed mice are the most common animal reservoirs. In California, the Western gray squirrel carries the bacterium. Horses, dogs and other domesticated animals can also carry ticks. Different ticks carry different illnesses so depending on where you live or travel, the TBI can vary. Black legged ticks can transmit Lyme disease as well as Anaplasmosis, Ehrlichiosis, Borrelia miyamotoi and Babesiosis, a few of the more familiar Lyme co-infections. Fifty percent or more of patients with Lyme disease are found to have co-infections when tested. The American dog tick and the Rocky Mountain wood tick carry Rocky Mountain Spotted Fever. Tularemia is a potentially serious illness that occurs naturally in the United States and can be transmitted by American dog ticks, as well as by biting flies or infected animals. Bartonella, not known to be transmitted by ticks, can be passed to humans via cat bites or cat scratches and infection with it is known as Cat Scratch Disease. Dogs carry a different type of Bartonella. Mosquitoes, sand flies, fleas, exposure to flea infested animals and the human body louse can all transmit Bartonella. Bartonella is difficult to detect on testing and it is not included in the CDC surveillance data for tick testing so we really do not know the true prevalence of this disease. Black legged ticks have a two to three year life cycle with four life stages: egg, larva, nymph and adult. Larval ticks feed on rodents and then become nymphs. Nymphs feed on small animals and humans and then become adult ticks. Adult ticks feed on deer. Larvae are the size of a grain of sand. Nymphs are the size of a poppy seed and adult ticks are about the size of an apple seed. When a tick bites, it swells so much that it sometimes can become unrecognizable. Ticks also secrete an anesthetic when they bite so many tick bites go unnoticed as a result. Many people mistakenly believe that Lyme disease cannot be transmitted when a tick has been attached for less than 24 hours. This is incorrect. Several animal studies have documented that although the risk of Lyme disease is low for attachment times less than 24 hours, the risk is not zero. Also, people with weakened immune systems can be at increased risk of disease when bitten. Symptoms of tick borne illnesses are many and varied and involve multiple systems depending on the specific disease. Anxiety, depression, headache, sleep disturbances, numbness, tingling, brain fog and cognitive dysfunction can result. Also, cardiac symptoms such as an irregular heart rhythm, chest pain and heart failure can all be due to TBI. Because the most common symptoms are fever, fatigue, and body aches it is difficult to diagnose and distinguish from other illnesses, especially the flu. The flu typically presents in the fall, winter or early spring so any “summer flu” always warrants investigation into TBI as the underlying cause. Early detection and early treatment are crucial in managing these illnesses effectively. Some signs and symptoms can develop months to years after the initial time of exposure adding to the complexity of diagnosis. Chronic or recurrent injury, illness or infection should also alert one to the possibility of TBI. Borrelia burgdorferi also has a wide range of survival mechanisms once it is inside the body to avoid and evade the immune system. These tactics contribute to the difficulty in diagnosing and treating this disease. One such strategy is the proteins found in tick saliva have been shown to inhibit the complement system which is the first line of defense implemented by the immune system to protect the host against pathogens. The organism is also pleomorphic which allows it to change its form based upon various environmental conditions. Its most common form is the spirochete, but B. burgdorferi can exist as round bodies or in a biofilm which protects the bacteria from environmental stresses like antibiotics and the immune system by surrounding the cells with a slime like material. It is important when treating Lyme disease to address all these different forms. There are 3 stages of Lyme disease. Stage 1 is early localized disease which can present within hours, days or weeks after a bite as a flu-like illness with headache, stiff neck, joint and/or muscle pain, swollen lymph glands and a sore throat. Each of these symptoms alone or in some combination can be a sign of early localized disease and because they are nonspecific, misdiagnosis is possible. The classic bull’s eye rash, known as erythema migrans is diagnostic of Lyme disease and only seen in about 27-40% of patients. Rashes from TBI can take alternate forms. Solid lesions, blue-purple hues, and crusted or blistering lesions have all been documented. A rash can appear at the site up to 30 days after the bite, with the average being about 7 days. Stage 2 is known as early disseminated infection and can occur several weeks to months after a bite. It can present with flu-like illness, skin rashes, headaches, fatigue, pain, weakness, numbness in the extremities, facial palsy, and it can cause Lyme carditis with chest pain and palpitations. Stage 3 is known as late disseminated disease and can develop years after the infected tick bite. Patients in this stage can develop Lyme arthritis, neurologic and cardiac symptoms including headaches, migraines, a stiff, aching, creaking, cracking neck, vertigo, dizziness, migratory pains that come and go, sleep disturbances, chronic fatigue, abnormal heart rhythms, heart block, brain fog, issues with memory, processing and concentration and peripheral neuropathy. Tick borne illness can mimic a variety of other illnesses and autoimmune disease can be triggered by TBI, therefore, it is imperative that we test for TBI in all symptomatic patients and those with autoimmune illness. If you see a tick bite, or you have unexplained symptoms, please contact a Lyme literate doctor as these clinicians are best equipped to give you the necessary care and treatment. The longer that tick borne illness remain untreated, the harder it can be to treat. The best approach to any vector borne illness is prevention which involves taking precautions to avoid being bitten by infected vectors. This can include using insect repellent, wearing protective clothing, and staying in well-screened areas. The use of mosquito nets while sleeping and eliminating areas of standing water on properties can also help to prevent mosquito breeding and exposure. According to the CDC, Lyme disease is a clinical diagnosis which means that symptoms, medical history, history of a tick bite, history of high risk behaviors such as hiking, gardening, landscaping and geographic location are all enough to make the diagnosis. Testing can help to support the diagnosis but should not be the sole determinant of diagnosis. Fifty percent of tests can be falsely negative. As a result, getting quality testing that is interpreted by a Lyme literate doctor is extremely important. Treatment of Tick Borne Illness can vary depending on how quickly it is discovered, how severe the symptoms are and what TBI has been contracted. For every tick borne illness, it is important to support the body by maintaining a healthy lifestyle, eating nutritious foods that come directly from nature, drinking clean water, getting seven to nine hours of restorative sleep, managing stress, making sure that your physical environment is free of chemicals by choosing “healthy” personal care and cleaning products and doing daily exercise if possible. Some Lyme patients are so severely compromised that they are unable to exercise. There is no one size fits all when it comes to treatment, even therapeutic lifestyle changes. Additionally, filtering your air, addressing any visible mold and looking for mold in areas of previous water damage is also vital to the process as this can slow recovery in TBI patients. The goal is to reduce as many factors as possible that can cause or contribute to inflammation. Doing so gives the body a better chance to fight the infection. Antibiotics are often the standard approach for acute illness, but can be used in chronic illness as well. There are also herbal remedies that are highly effective on their own or in combination with antibiotics to treat both acute and chronic disease. Tick borne illnesses can present with mild symptoms for some, while others can have their quality of life severely impacted. Symptoms can be confusing and difficult to navigate, especially when dealing with an inflamed and foggy brain. Although the journey can be long, overwhelming and sometimes feel bleak, there are ways to improve symptoms and regain your quality of life with the right help.