Genes shape our response to Covid virus
From infections with no symptoms to why men are more likely to be hospitalized in the ICU and die of COVID-19, new research shows that your genes play a significant role
Early in the pandemic, genetic research focused on the virus because it was readily available. Plus, the virus contains only 30,000 bases in a dozen functional genes, so it's relatively easy and affordable to sequence. Additionally, the rapid mutation of the virus and its ability to escape antibody control fueled waves of different variants and provided a reason to follow viral genetics.
In comparison, there are many more genes of the human immune system and cellular functions that affect viral replication, with about 3.2 billion base pairs. Human studies require samples from large numbers of people, the analysis of each sample is vastly more complex, and sophisticated computer analysis often is required to make sense of the raw data. All of this takes time and large amounts of money, but important findings are beginning to emerge.
Asymptomatics
About half the people exposed to SARS-CoV-2, the virus that causes the COVID-19 disease, never develop symptoms of this disease, or their symptoms are so mild they often go unnoticed. One piece of understanding the phenomena came when researchers showed that exposure to OC43, a common coronavirus that results in symptoms of a cold, generates immune system T cells that also help protect against SARS-CoV-2.
Jill Hollenbach, an immunologist at the University of California at San Francisco, sought to identify the gene behind that immune protection. Most COVID-19 genetic studies are done with the most seriously ill patients because they are hospitalized and thus available. “But 99 percent of people who get it will never see the inside of a hospital for COVID-19,” she says. “They are home, they are not interacting with the health care system.”
Early in the pandemic, when most labs were shut down, she tapped into the National Bone Marrow Donor Program database. It contains detailed information on donor human leukocyte antigens (HLAs), key genes in the immune system that must match up between donor and recipient for successful transplants of marrow or organs. Each HLA can contain alleles, slight molecular differences in the DNA of the HLA, which can affect its function. Potential HLA combinations can number in the tens of thousands across the world, says Hollenbach, but each person has a smaller number of those possible variants.
She teamed up with the COVID-19 Citizen Science Study a smartphone-based study to track COVID-19 symptoms and outcomes, to ask persons in the bone marrow donor registry about COVID-19. The study enlisted more than 30,000 volunteers. Those volunteers already had their HLAs annotated by the registry, and 1,428 tested positive for the virus.
Analyzing five key HLAs, she found an allele in the gene HLA-B*15:01 that was significantly overrepresented in people who didn’t have any symptoms. The effect was even stronger if a person had inherited the allele from both parents; these persons were “more than eight times more likely to remain asymptomatic than persons who did not carry the genetic variant,” she says. Altogether this HLA was present in about 10 percent of the general European population but double that percentage in the asymptomatic group. Hollenbach and her colleagues were able confirm this in other different groups of patients.
What made the allele so potent against SARS-CoV-2? Part of the answer came from x-ray crystallography. A key element was the molecular shape of parts of the cold virus OC43 and SARS-CoV-2. They were virtually identical, and the allele could bind very tightly to them, present their molecular antigens to T cells, and generate an extremely potent T cell response to the viruses. And “for whatever reasons that generated a lot of memory T cells that are going to stick around for a long time,” says Hollenbach. “This T cell response is very early in infection and ramps up very quickly, even before the antibody response.”
Understanding the genetics of the immune response to SARS-CoV-2 is important because it provides clues into the conditions of T cells and antigens that support a response without any symptoms, she says. “It gives us an opportunity to think about whether this might be a vaccine design strategy.”
Dead men
A researcher at the Leibniz Institute of Virology in Hamburg Germany, Guelsah Gabriel, was drawn to a question at the other end of the COVID-19 spectrum: why men more likely to be hospitalized and die from the infection. It wasn't that men were any more likely to be exposed to the virus but more likely, how their immune system reacted to it
Several studies had noted that testosterone levels were significantly lower in men hospitalized with COVID-19. And, in general, the lower the testosterone, the worse the prognosis. A year after recovery, about 30 percent of men still had lower than normal levels of testosterone, a condition known as hypogonadism. Most of the men also had elevated levels of estradiol, a female hormone (https://pubmed.ncbi.nlm.nih.gov/34402750/).
Every cell has a sex, expressing receptors for male and female hormones on their surface. Hormones docking with these receptors affect the cells' internal function and the signals they send to other cells. The number and role of these receptors varies from tissue to tissue.
Gabriel began her search by examining whole exome sequences, the protein-coding part of the genome, for key enzymes involved in the metabolism of sex hormones. The research team quickly zeroed in on CYP19A1, an enzyme that converts testosterone to estradiol. The gene that produces this enzyme has a number of different alleles, the molecular variants that affect the enzyme's rate of metabolizing the sex hormones. One genetic variant, CYP19A1 (Thr201Met), is typically found in 6.2 percent of all people, both men and women, but remarkably, they found it in 68.7 percent of men who were hospitalized with COVID-19.
Lung surprise
Lungs are the tissue most affected in COVID-19 disease. Gabriel wondered if the virus might be affecting expression of their target gene in the lung so that it produces more of the enzyme that converts testosterone to estradiol. Studying cells in a petri dish, they saw no change in gene expression when they infected cells of lung tissue with influenza and the original SARS-CoV viruses that caused the SARS outbreak in 2002. But exposure to SARS-CoV-2, the virus responsible for COVID-19, increased gene expression up to 40-fold, Gabriel says.
Did the same thing happen in humans? Autopsy examination of patients in three different cites found that “CYP19A1 was abundantly expressed in the lungs of COVID-19 males but not those who died of other respiratory infections,” says Gabriel. This increased enzyme production led likely to higher levels of estradiol in the lungs of men, which “is highly inflammatory, damages the tissue, and can result in fibrosis or scarring that inhibits lung function and repair long after the virus itself has disappeared.” Somehow the virus had acquired the capacity to upregulate expression of CYP19A1.
Only two COVID-19 positive females showed increased expression of this gene. The menopause status of these women, or whether they were on hormone replacement therapy was not known. That could be important because female hormones have a protective effect for cardiovascular disease, which women often lose after going through menopause, especially if they don’t start hormone replacement therapy. That sex-specific protection might also extend to COVID-19 and merits further study.
The team was able to confirm their findings in golden hamsters, the animal model of choice for studying COVID-19. Testosterone levels in male animals dropped 5-fold three days after infection and began to recover as viral levels declined. CYP19A1 transcription increased up to 15-fold in the lungs of the male but not the females. The study authors wrote, “Virus replication in the male lungs was negatively associated with testosterone levels.”
The medical community studying COVID-19 has slowly come to recognize the importance of adipose tissue, or fat cells. They are known to express abundant levels of CYP19A1 and play a significant role as metabolic tissue in COVID-19. Gabriel adds, “One of the key findings of our study is that upon SARS-CoV-2 infection, the lung suddenly turns into a metabolic organ by highly expressing” CYP19A1.
She also found evidence that SARS-CoV-2 can infect the gonads of hamsters, thereby likely depressing circulating levels of sex hormones. The researchers did not have autopsy samples to confirm this in humans, but others have shown that the virus can replicate in those tissues.
A possible treatment
Back in the lab, substituting low and high doses of testosterone in SARS-COV-2 infected male hamsters had opposite effects depending on testosterone dosage used. Gabriel says that hormone levels can vary so much, depending on health status and age and even may change throughout the day, that “it probably is much better to inhibit the enzyme” produced by CYP19A1 than try to balance the hormones.
Results were better with letrozole, a drug approved to treat hypogonadism in males, which reduces estradiol levels. The drug also showed benefit in male hamsters in terms of less severe disease and faster recovery. She says more details need to be worked out in using letrozole to treat COVID-19, but they are talking with hospitals about clinical trials of the drug.
Gabriel has proposed a four hit explanation of how COVID-19 can be so deadly for men: the metabolic quartet. First is the genetic risk factor of CYP19A1 (Thr201Met), then comes SARS-CoV-2 infection that induces even greater expression of this gene and the deleterious increase of estradiol in the lung. Age-related hypogonadism and the heightened inflammation of obesity, known to affect CYP19A1 activity, are contributing factors in this deadly perfect storm of events.
Studying host genetics, says Gabriel, can reveal new mechanisms that yield promising avenues for further study. It’s also uniting different fields of science into a new, collaborative approach they’re calling “infection endocrinology,” she says.
The Friday Five: An mRNA vaccine works against cancer, new research suggests
The Friday Five covers five stories in research that you may have missed this week. There are plenty of controversies and troubling ethical issues in science – and we get into many of them in our online magazine – but this news roundup focuses on scientific creativity and progress to give you a therapeutic dose of inspiration headed into the weekend.
Listen on Apple | Listen on Spotify | Listen on Stitcher | Listen on Amazon | Listen on Google
Here are the promising studies covered in this week's Friday Five:
- An mRNA vaccine that works against cancer
- These cameras inside the body have an unusual source of power
- A new theory for what causes aging
- Can bacteria make you excited to work out?
- Why women get Alzheimer's more often than men
Last minute holiday gifts for the bio-inspired
“Merry Christmas! Isn’t it fun to say Merry Christmas to everyone? Time for a party and presents and things that make children happy and give their hearts wings!” go the lyrics of the popular Christmas poem. But adults (of various religions) need their gifts this time of year, too. For the biologically inspired big children, the process of finding the right fit can be daunting. To inform your choices in both conventional and unconventional ways, Leaps.org is presenting a roundup of the coolest bio-products related to health, nutrition, gaming, lifestyle and more.
AYO Circadian Light Therapy Wearable
We don’t hear it tick, but we have our own clock inside our body–more precisely, circadian clocks. Our cells contain tiny molecular clocks that keep track of our circadian rhythms, or our sleep and metabolism pattern and activity levels, on a daily basis. Chronic circadian disruptions can lead to sleep disorders, poor energy levels, weight gain, lousy mood, and sped-up aging, as well as increased risk for every “modern” disease out there, from diabetes to cancer.
Now, high-tech glasses have been developed that attempt to mimic the benefits of sunlight. In the morning and afternoon, these glasses shed blue light into your eyes to stimulate the master clock at the base of your brain for less drowsiness. The technology's design draws from an area of research, chronobiology, that received a Nobel Prize in 2017 and has become increasingly active in recent years.
“We have been developing and testing the AYO Circadian Health solution for the past five years in collaboration with some of the world's leading experts and researchers in chronobiology, light therapy and health,” said Alexander Dimitrov, co-creator of AYO. “We have done studies with over 25,000 participants, and over one million light sessions,” Dimotrov continued, partnering with institutions such as Mount Sinai Hospital, City of Hope and the U.S. Department of Defense.
The technology could fundamentally reshape the way we view sleep, health and our daily calendars. And, when connecting to a mobile app, the glasses could minimize circadian disruptions for travelers between conflicting time zones.
($269)
myDNAge Test
It's not easy for many people to break free of their attachment to the concept of chronological age, which counts years by how many times we’ve circled the sun since the day we were born. Society lumps us all into one age bracket according to our date of birth but, lately, research is suggesting that we should do some serious deconditioning. According to these studies, the more accurate measure is your biological age, a measurement based on various biomarkers of the body’s overall health and resilience, regardless of your calendar age.
If you want to find out your “true” biological age, myDNAge is a test that focuses on epigenetics, or patterns of changes in DNA methylation, with some initial research pointing to its accuracy. It offers a snapshot of your epigenetic age as well as key biomarkers related to your metabolism, risk of Alzheimer's and more, according to Xiaojing Yang, group leader of epigenetics at myDNAge. “You can perform tests six to 12 months [apart] to track the impact of lifestyle changes,” Yang said. The kit could be a useful tool both for citizen scientists and biohacking veterans.
($299 for one kit–Use code NEWYEARNEWME to receive 50% off a second kit)
Prairie Sky Yak Cheese
Do you love cheese? Do you love exotic cheese? Do you have an interest in preserving biological and genetic diversity? If you answered yes to all three questions, yak cheese was made for you. This type of cheese typically comes from a free-range yak living 13,000 feet above surface level in the Tibetan Himalayas, a relative of the endangered Wild yak. (North America is home to at least 5,000 registered yaks.)
“When I learned that we had a piece of rare biodiversity to be preserved for future generations, I realized that the yak in North America needed a job,” said Nicole Geijer Porter, president of World Heritage Yak Conservancy (WHYC), an organization formed to protect heritage yak “If an animal cannot be beneficial to the rancher in some way, exclusively as pets and lawn ornaments, they will go extinct. Raised for meat they are often hybridized with cattle to grow bigger and faster, so they will also go extinct,” said Porter, an epigeneticist turned yak herder.
Each slice of cheese and piece of butter supports the genetic testing and tracking of Tibetan yak. (You can become a member of WHYC through the Adopt-A-Yak program). “This project is also of biological importance because of the low methane emission research on yak, and the high nutritional content of the milk and cheese,” said Porter.
As for flavor, the Prairie Sky Yak Gruyere is a semi-hard cheese with a nutty taste sometimes compared to chocolate; Tomme de Savoie is a semi-soft Alpine cheese reminiscent of a washed rind muenster; and the Yak Cheddar is made with yak milk following the classic English recipe from Wells Cathedral, with earthly and pungent flavors.
(Various prices; $59.95 for the Three Yak Cheese Flight Gift Box, $139.95 for the Regional Himalayan Yak Cheddar Gift Basket and more)
Bite Toothpaste Bits
The price of a healthy smile is steep. Each year over one billion plastic toothpaste tubes are thrown out, over 50 Empire State Buildings worth of these tubes end up in landfills or oceans, and many animals suffer and die each year in cruel tests for improving oral care in people.
Sustainable oral care is both an act of self-love and giving back to the environment. Bite is a toothpaste that boasts about its green practices for a reason: it uses recyclable glass bottles with aluminum lids that break down into sand after they’ve been used. For shipping, Bite uses kraft envelopes padded with recycled and compostable newspapers, and its boxes are made of fully recycled, corrugated cardboard and sealed with paper tape. Bite refills come in 100% home compostable pouches every four months (still no plastic).
Sustainability aside, there may be an element of fun to Bite – as you brush, a mint foam forms “like magic,” the company claims.
Fractional Laser Treatment for Skin
The environment is hard on our skin: from ultraviolet rays to pollution, a constant oxidative war is waged upon it, leading to loss of collagen and damage to the barrier function of the skin. A fractional laser treatment is a type of laser skin resurfacing procedure that essentially traumatizes the skin – in a good way - through subjecting a small area of it to tiny amounts of laser energy. The laser penetrates the second layer of skin, the dermis, leading to skin exfoliation, which stimulates collagen and elastin production.
The treatment may help with soothing acne scarring, correcting uneven skin tone and texture, and reducing wrinkles and fine lines, sun damage and age spots. Recent research suggests the fractional laser can help with improving skin elasticity and reducing the amount and depth of wrinkles, though there’s little to no evidence for any benefits for eyebags, dark circles, discolorations within the eye area and water retention.
(Typically, a single fractional laser treatment costs $750 for a small area, $1500 for a full facial treatment, and $2000 for full face.)
Gadgets and Apps to Measure Your Heart Rate Variability
Heart rate variability may sound like a condition that requires immediate medical treatment, but the more you have of it, the better for your health. Although you may think of the heart as a steadily beating metronome, there are actually small differences in the amount of time between each beat. These differences are called HRV, and having more HRV has been linked to better fitness and fewer diseases.
HRV is easy to measure with a range of gadgets on the market, including Fitbits and Oura Rings. Which product floats your boat is a matter of personal preference, but the Polar H10 chest strap offers some advantages. For example, you can measure your HRV with the Polar H10 while walking around, unlike some devices that require you to stay still while taking a reading.
Plus, the Polar sensor pairs with free apps such as Elite HRV that are great for tracking how your HRV changes over time. "HRV really helps you gauge if you're moving in a positive or negative direction" with your health, says Jason Moore, the CEO and founder of Elite HRV and Spren. Have fun experimenting over the holidays with different lifestyle habits that are associated with higher HRV, some studies show, such as intermittent fasting, regular exercise and just getting more sleep.
($89 for the Polar H10, $0 for the Elite HRV app)
FoodMarble AIRE2
Its predecessor, FOODMarble AIRE1 was a pocket-size breath-testing device that measured hydrogen on the breath. More hydrogen means less digestion, and the AIRE1 used advanced breathalyzer technology to figure out what exactly is going on with the gut. Now, the company has launched FoodMarble AIRE2, which also measures methane alongside with hydrogen. High levels of methane in the body may cause abdominal pain, bloating and constipation, cirrhosis of the liver and chronic pancreatitis. The AIRE2 also comes with haptic feedback to make it easier to use.
Research suggests that these breath tests are valid as at-home diagnostic tools for many digestive conditions. To get the most accurate results, though, it’s important to closely follow the recommended protocol - for example, you can’t eat or drink anything for 10 to 12 hours before the test.
($229)
Adventurist Backpack’s Classic Backpack
The Classic backpack is a perfect option for life science aficionados who enjoy getting outside and exploring in nature. Padding in the front and back provides extra protection for camera gear, laptop, and other electronics, and it's completely water-resistant so you can get outside in winter weather.
Nobility points: Adventurist Backpack Co. is partnered with national non-profit Feeding America, and every backpack sold helps provide 25 meals to families in need across the U.S.
($65)
This Saves Lives
Speaking of nobility points, you could load your new backpack with a food choice that helps feed others as well. In 2013, actors Kristin Bell, Ryan Devlin, Ravi Patel and Todd Grinnell teamed up to start This Saves Lives, which makes power bars full of vitamins and nutrients, and the company has a unique business model: for every bar you buy, a packet of food is sent to a child in need. In addition to offering essential nutrients, the bars are non-GMO, kosher and gluten-free. Note: This Saves Lives is owned by the same company, GOOD Worldwide, that owns Leaps.org.
(Wild Blueberry & Pistachio bars, $23.99)
NADI X Pants
Even if you’re a yoga zealot enjoying the benefits to your strength, balance and flexibility, chances are you're performing the movements sort of askew. Wearable technology wants to improve your yoga posture and these sleek yoga pants called NADI X have subtle electronic sensors that track how you place your hands, rotate your hips, and align your back. The leggings use haptic feedback (or vibrations on your skin) to slowly guide you into correct alignment. You can also combine the wearable with an app that contains 40 poses and fitting music. Even if you aren't into yoga, you could use the pants for a perfect stretching session. If you do use it for yoga poses, the pants will “speak” to you, letting out a soothing "om" sound once everything is perfect.
Meta Quest Pro VR headset
When it comes to perfecting virtual reality (VR), the Meta Quest Pro VR headset is one step ahead the rest. In a vibrant 3D virtual space, your Meta avatar has the ability to translate your real-life facial expressions into the virtual realm so the experience can feel more personal, while controllers track your movement and use haptic feedback to translate your hand gestures and finger actions into VR as well. Unlike its Quest 2 headset, Meta markets this Quest Pro headset, which was just released in October, as a great tool for work and business meetings, but you can also use it to play games, watch movies, or download fitness apps or mental-health related apps – some of which are designed to help you get boxing workouts with long-distance friends, fight your fear of heights or meditate in outer space.
Rouge Sur Mesure Custom Lip Color Creator
Beauty and artificial intelligence (AI) complement each other well in the new Yves Saint Laurent lip personalized color – which wants to put the final nail on the coffin of generic lipsticks. This is a lipstick printer at its core. You pair a device to your smartphone and then insert three lipstick cartridges into the base, each of which comes with a color palette (all four could create up to 4,000 lipstick shades). Particularly charming is the fact that you can take a photo of your outfit, and the app will suggest shades that match or clash it.
($299, cartridges $89 each)
Dairy-Free Cream Cheese and Meatless Breakfast Patties
On the environmental front again, meatless patties and dairy-free cream cheese constitute conscientious and delicious choices for vegans, vegetarians and pretty much anyone else. Chicago-based Nature's Fynd is worth checking out. It uses a microbe named Fusarium strain flavolapis, which has origins in an acidic hot spring at Yellowstone National Park.
“We use this remarkable microbe to grow Fy — a nutritional fungi protein that’s made into a wide variety of delicious and sustainable foods,” says Karuna Rawal, Nature’s Fynd CMO. Fy is grown via a breakthrough fermentation process using a fraction of the water, land, and energy compared to traditional protein sources.
It’s a sustainable way to grow food for Earth’s population,” but Nature’s Fynd isn’t just concentrating on Earth. The company recently partnered with NASA to send Fy to space. “As long as there’s an appropriately controlled environment, we can grow Fy anytime, anywhere. It could be a nutritious food source for astronauts on deep space missions," said Rawal.
CBD Oil
Biologically curious people may be especially interested in trying cannabinoid (CBD) oil. CBD is a natural and safe substance found in cannabis, which has been found to tackle anxiety and depression, reduce symptoms of post-traumatic stress disorder, help manage chronic pain and migraines, improve sleep patterns, and keep panic attacks at bay. Kanibi’s Isolate CBD Oil Tincture is a good choice as it is cinnamon-flavored and made in an FDA-inspected facility.
($109--25% off on your first order)
Govee RGBIC Floor Lamp
Another winner for anyone who's been hearing about the health benefits of obeying your circadian rhythms: "RGB" lights, or red-green-blue lights that can be operated by remote control to shine bright blue light during the day and then, with a few touches of your phone, bathe you in warmer, red light to get you ready for bed. Look for RGB bulbs to stick into the light fixtures you already have, or you could opt for the Govee floor lamp that syncs with an app on your phone (or Alexa) for circadian color changing. You can also put it on party mode and watch it shift across 16 million color shades in response to the rhythms and beats of Cuddle Up, Cozy Down Christmas and Hanukkah Oh Hanukkah.
($99)
PackPoint
If you suffer from packing anxiety (or incompetence), an app may take away the pain. PackPoint is an app that builds your packing list according to trip type, activities and weather. You add your trip details, select activities (fancy dinner, business meeting, or even workout are some examples), and PackPoint tells you what you need to bring to your destination. The app is free, but upgrading to Premium for a small fee lets you add your own activities and packing list items.
(Free, Premium Package $2.99)
Eternity Rose
Roses symbolize love, passion, innocence, friendship, and the disarming power of natural beauty. They wilt fast, though, and their spectacle is an unsettling reminder of the fragility of beauty and existence. Unless you dip the rose in 24 karat gold.
The Eternity Rose is put through an intricate three-month process of electroplating, or coating the rose with copper and then with other metals in micro-thin layers. You won’t have to see your flowers sag after a few days because these roses never die. The glitter of gold atop the natural rose (or platinum or silver–whatever you prefer) will fit right in with the Christmas Eve ambiance.
($169 for the gold rose)