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.
When Erika Schreder’s 14-year-old daughter, who is Black, had her curly hair braided at a Seattle-area salon two or three times recently, the hairdresser applied a styling gel to seal the tresses in place.
Schreder and her daughter had been trying to avoid harmful chemicals, so they were shocked to later learn that this particular gel had the highest level of formaldehyde of any product tested by the Washington State Departments of Ecology and Health. In January 2023, the agencies released a report that uncovered high levels of formaldehyde in certain hair products, creams and lotions marketed to or used by people of color. When Schreder saw the report, she mentioned it to her daughter, who told her the name of the gel smoothed on her hair.
“It was really upsetting,” said Schreder, science director at Toxic-Free Future, a Seattle-based nonprofit environmental health research and advocacy organization. “Learning that this product used on my daughter’s hair contained cancer-causing formaldehyde made me even more committed to advocating for our state to ban toxic ingredients in cosmetics and personal care products.”
In 2013, Toxic-Free Future launched Mind the Store to challenge the nation’s largest retailers in adopting comprehensive policies that eliminate toxic chemicals in their personal care products and packaging, and develop safer alternatives.
Now, more efforts are underway to expose and mitigate the harm in cosmetics, hair care and other products that children apply on their faces, heads, nails and other body parts. Advocates hope to raise awareness among parents while prompting manufacturers and salon professionals to adopt safer alternatives.
A recent study by researchers at Columbia University Mailman School of Public Health and Earthjustice, a San Francisco-based nonprofit public interest environmental law organization, revealed that most children in the United States use makeup and body products that may contain carcinogens and other toxic chemicals. In January, the results were published in the International Journal of Environmental Research and Public Health. Based on more than 200 surveys, 70 percent of parents in the study reported that their children 12 or younger have used makeup and body products marketed to youth — for instance, glitter, face paint and lip gloss.
Childhood exposure to harmful makeup and body product ingredients can also be considered an environmental justice issue, as communities of color may be more likely to use these products.
“We are concerned about exposure to chemicals that may be found in cosmetics and body products, including those that are marketed toward children,” said the study’s senior author, Julie Herbstman, a professor and director of the Columbia Center for Children's Environmental Health. The goal of the survey was to try to understand how much kids are using cosmetic and body products and when, how and why they are using them.
“There is widespread use of children’s cosmetic and body products, and kids are using them principally to play,” Herbstman said. “That’s really quite different than how adults use cosmetic and body products.” Even with products that are specifically designed for children, “there’s no regulation that ensures that these products are safe for kids.” Also, she said, some children are using adult products — and they may do so in inadvisable ways, such as ingesting lipstick or applying it to other areas of the face.
Earlier research demonstrated that beauty and personal care products manufactured for children and adults frequently contain toxic chemicals, such as lead, asbestos, PFAS, phthalates and formaldehyde. Heavy metals and other toxic chemicals in children’s makeup and body products are particularly harmful to infants and youth, who are growing rapidly and whose bodies are less efficient at metabolizing these chemicals. Whether these chemicals are added intentionally or are present as contaminants, they have been associated with cancer, neurodevelopmental harm, and other serious and irreversible health effects, the Columbia University and Earthjustice researchers noted.
“Even when concentrations of individual chemicals are low in products, the potential for interactive effects from multiple toxicants is important to take into consideration,” the authors wrote in the journal article. “Allergic reactions, such as contact dermatitis, are some of the most frequently cited negative health outcomes associated with the use of cosmetics.”
Children’s small body side, rapid growth rate and immature immune systems are biologically more prone to the effects of toxicants than adults.
Adobe Stock
In addition to children’s rapid growth rate, the study also reported that their small body size, developing tissues and organs, and immature immune systems are biologically more prone to the effects of toxicants than adults. Meanwhile, the study noted, “childhood exposure to harmful makeup and body product ingredients can also be considered an environmental justice issue, as communities of color may be more likely to use these products.”
Although adults are the typical users of cosmetics, similar items are heavily marketed to youth with attention-grabbing features such as bright colors, animals and cartoon characters, according to the study. Beyond conventional makeup such as eyeshadow and lipstick, children may apply face paint, body glitter, nail polish, hair gel and fragrances. They also may frequent social media platforms on which these products are increasingly being promoted.
Products for both children and adults are currently regulated by the U.S. Food and Drug Administration under the Federal Food, Drug, and Cosmetic Act of 1938. Also, the Fair Packaging and Labeling Act of 1967 directs the Federal Trade Commission and the FDA “to issue regulations requiring that all ‘consumer commodities’ be labeled to disclose net contents, identity of commodity, and name and place of business of the product's manufacturer, packer, or distributor.” As the Columbia University and Earthjustice authors pointed out, though, “current safety regulations have been widely criticized as inadequate.”
The Personal Care Products Council in Washington, D.C., “fundamentally disagrees with the premise that companies put toxic chemicals in products produced for children,” industry spokeswoman Lisa Powers said in an email. Founded in 1894, the national trade association represents 600 member companies that manufacture, distribute and supply most personal care products marketed in the United States.
No category of consumer products is subject to less government oversight than cosmetics and other personal care products. -- Environmental Working Group.
“Science and safety are the cornerstones of our industry,” Powers stated. For more than a decade, she wrote, “the [Council] and our member companies worked diligently with a bipartisan group of congressional leaders and a diverse group of stakeholders to enhance the effectiveness of the FDA regulatory authority and to provide the safety reassurances that consumers expect and deserve.”
Powers added that the “industry employs and consults thousands of scientific and medical experts” who study the impacts of cosmetics and personal care products and the ingredients used in them. The Council also maintains a comprehensive database where consumers can look up science and safety information on the thousands of ingredients in sunscreens, toothpaste, shampoo, moisturizer, makeup, fragrances and other products.
However, the Environmental Working Group, which empowers consumers with breakthrough research to make informed choices about healthy living, believes the regulations are still not robust enough. “No category of consumer products is subject to less government oversight than cosmetics and other personal care products,” states the organization’s website. “Although many of the chemicals and contaminants in cosmetics and personal care products likely pose little risk, exposure to some has been linked to serious health problems, including cancer.”
The group, which operates the Skin Deep Database noted that “since 2009, 595 cosmetics manufacturers have reported using 88 chemicals, in more than 73,000 products, that have been linked to cancer, birth defects or reproductive harm.”
But change, for both adults and kids, is on the horizon. The Modernization of Cosmetics Regulation Act of 2022 significantly expanded the FDA’s authority to regulate cosmetics. In May 2023, Washington state adopted a law regulating cosmetics and personal care products. The Toxic-Free Cosmetics Act (HB 1047) bans chemicals in beauty and personal care products, such as PFAS, lead, mercury, phthalates and formaldehyde-releasing agents. These bans take effect in 2025, except for formaldehyde releasers, which have a phased-in approach starting in 2026.
Industry and advocates view this as a positive development. Powers, the spokesperson, praised “the long-awaited” Modernization Cosmetics Regulation Act of 2022, which she said, “advances product safety and innovation.” Jen Lee, chief impact officer at Beautycoutner, a company that sells personal care products, also welcomes the change. “We were proud to support the Washington Toxic-Free Cosmetics Act (HB 1047) by mobilizing our community of Brand Advocates who reside in Washington State,” Lee said. “Together, they made their voices heard by sending over 1,000 emails to their state legislators urging them to support and pass the bill.”
Laurie Valeriano, executive director of Toxic-Free Future, praised the upcoming Washington state law as “a huge win for public health and the environment that will have impacts that ripple across the nation.” She added that “companies won’t make special products for Washington state.” Instead, “they will reformulate and make products safer for everyone” — adults and children.
You shouldn’t have to be a toxicologist to shop for shampoo. -- Washington State Rep. Sharlett Mena
The new legislation will require Washington state agencies to assess the hazards of chemicals used in products that can impact vulnerable populations, while providing support for small businesses and independent cosmetologists to transition to safer products.
The Toxic-Free Future team lauds the Cosmetics Act, signed in May 2023.
Courtesy Toxic-Free Future
“When we go to a store, we assume the products on the shelf are safe, but this isn’t always true,” said Washington State Rep. Sharlett Mena, a Democrat serving in the 29th Legislative District (Tacoma), who sponsored the law. “I introduced this bill (HB 1047) because currently, the burden is on the consumer to navigate labels and find safe alternatives. You shouldn’t have to be a toxicologist to shop for shampoo.”
The new law aims to protect people of all ages, but especially youth. “Children are more susceptible to the impacts of toxic chemicals because their bodies are still developing,” Mena said. “Lead, for example, is significantly more hazardous to children than adults. Also, since children, unlike adults, tend to put things in their mouths all the time, they are more exposed to harmful chemicals in personal care and other products.”
Cosmetologists and hair professionals are taking notice. “Safety should be the practitioner’s number one concern” in using products on small children, said Anwar Saleem, a hair stylist, instructor and former salon owner in Washington, D.C., who is chairman of the D.C. Board of Barbering and Cosmetology and president of the National Interstate Council of State Boards of Cosmetology. “There are so many products on the market that it can be confusing.”
Hair products designed and labeled for children's use often have milder formulations, but “every child is unique, and what works for one may not work for another,” Saleem said. He recommends doing a patch test, in which the stylist or cosmetologist dabs the product on a small, inconspicuous area of the scalp or skin and waits anywhere from an hour to a day to check for irritation before continuing to serve the client. “Performing a patch test, observing children's reactions to a product and adequately adjusting are essential.”
Saleem seeks products that are free from harsh chemicals such as sulfates, phthalates and parabens, noting that these ingredients can be irritating and drying to the hair and scalp. If a child has sensitive skin or allergies, Saleem opts for hypoallergenic products.
We also need to ensure that less toxic alternatives are available and accessible to all consumers. It’s often under-resourced, low-income populations who suffer the burden of environmental exposures and do not have access or cannot afford these safer alternatives. -- Lesliam Quirós-Alcalá.
Lesliam Quirós-Alcalá, an assistant professor in the department of environmental health and engineering at the Johns Hopkins Bloomberg School of Public Health, said current regulatory loopholes on product labeling still allow manufacturers to advertise their cosmetics and personal care products as “gentle” and “natural.” However, she said, those terms may be misleading as they don’t necessarily mean the contents are less toxic or harmful to consumers.
“We also need to ensure that less toxic alternatives are available and accessible to all consumers,” Quirós-Alcalá said, “as often alternatives considered to be less toxic come with a hefty price tag.” As a result, “it’s often under-resourced, low-income populations who suffer the burden of environmental exposures and do not have access or cannot afford these safer alternatives.”
To advocate for safer alternatives, Quirós-Alcalá suggests that parents turn to consumer groups involved in publicizing the harms of personal care products. The Campaign for Safe Cosmetics is a program of Breast Cancer Prevention Partners, a national science-based advocacy organization aiming to prevent the disease by eliminating related environmental exposures. Other resources that inform users about unsafe ingredients include the mobile apps Clearya and Think Dirty.
“Children are not little adults, so it’s important to increase parent and consumer awareness to minimize their exposures to toxic chemicals in everyday products,” Quirós-Alcalá said. “Becoming smarter, more knowledgeable consumers is the first step to protecting your family from potentially harmful and toxic ingredients in consumer products.”
A startup aims to make medicines in space
Story by Big Think
On June 12, a SpaceX Falcon 9 rocket deployed 72 small satellites for customers — including the world’s first space factory.
The challenge: In 2019, pharma giant Merck revealed that an experiment on the International Space Station had shown how to make its blockbuster cancer drug Keytruda more stable. That meant it could now be administered via a shot rather than through an IV infusion.
The key to the discovery was the fact that particles behave differently when freed from the force of gravity — seeing how its drug crystalized in microgravity helped Merck figure out how to tweak its manufacturing process on Earth to produce the more stable version.
Microgravity research could potentially lead to many more discoveries like this one, or even the development of brand-new drugs, but ISS astronauts only have so much time for commercial experiments.
“There are many high-performance products that are only possible to make in zero-gravity, which is a manufacturing capability that cannot be replicated in any factory on Earth.”-- Will Bruey.
The only options for accessing microgravity (or free fall) outside of orbit, meanwhile, are parabolic airplane flights and drop towers, and those are only useful for experiments that require less than a minute in microgravity — Merck’s ISS experiment took 18 days.
The idea: In 2021, California startup Varda Space Industries announced its intention to build the world’s first space factory, to manufacture not only pharmaceuticals but other products that could benefit from being made in microgravity, such as semiconductors and fiber optic cables.
This factory would consist of a commercial satellite platform attached to two Varda-made modules. One module would contain equipment capable of autonomously manufacturing a product. The other would be a reentry capsule to bring the finished goods back to Earth.
“There are many high-performance products that are only possible to make in zero-gravity, which is a manufacturing capability that cannot be replicated in any factory on Earth,” said CEO Will Bruey, who’d previously developed and flown spacecraft for SpaceX.
“We have a team stacked with aerospace talent in the prime of their careers, focused on getting working hardware to orbit as quickly as possible,” he continued.
“[Pharmaceuticals] are the most valuable chemicals per unit mass. And they also have a large market on Earth.” -- Will Bruey, CEO of Varda Space.
What’s new? At the time, Varda said it planned to launch its first space factory in 2023, and, in what feels like a first for a space startup, it has actually hit that ambitious launch schedule.
“We have ACQUISITION OF SIGNAL,” the startup tweeted soon after the Falcon 9 launch on June 12. “The world’s first space factory’s solar panels have found the sun and it’s beginning to de-tumble.”
During the satellite’s first week in space, Varda will focus on testing its systems to make sure everything works as hoped. The second week will be dedicated to heating and cooling the old HIV-AIDS drug ritonavir repeatedly to study how its particles crystalize in microgravity.
After about a month in space, Varda will attempt to bring its first space factory back to Earth, sending it through the atmosphere at hypersonic speeds and then using a parachute system to safely land at the Department of Defense’s Utah Test and Training Range.
Looking ahead: Ultimately, Varda’s space factories could end up serving dual purposes as manufacturing facilities and hypersonic testbeds — the Air Force has already awarded the startup a contract to use its next reentry capsule to test hardware for hypersonic missiles.
But as for manufacturing other types of goods, Varda plans to stick with drugs for now.
“[Pharmaceuticals] are the most valuable chemicals per unit mass,” Bruey told CNN. “And they also have a large market on Earth.”
“You’re not going to see Varda do anything other than pharmaceuticals for the next minimum of six, seven years,” added Delian Asparouhov, Varda’s co-founder and president.