The original Chinese version of this article was published in the September 2024 issue of Global Science (the Chinese edition of Scientific American).
In 1950, a 20-year-old British medical student named Roy Calne was on hospital duty when he encountered a young patient dying of kidney failure. As he looked on, powerless to help, a question arose in his mind. The son of a car mechanic, Calne wondered: if broken car parts can be replaced, why not human organs?
Nearly two decades later, by 1968, Calne had become a professor of surgery at the University of Cambridge, where he led the team that performed Europe’s first human liver transplant. He soon turned his attention to the challenge of multi-organ transplants, and that’s when he noticed something curious. In pigs undergoing experimental procedures, those that received a liver transplant seemed to escape the usual fate of immune rejection.
Calne found that if a recipient pig received a liver from a donor, either before or at the same time as a skin, kidney, or heart transplant from the same donor, the immune system’s attack on those organs was dramatically reduced. The grafts lasted significantly longer. Strangely, even if the liver was removed a week later, the protective effect remained. It was as if the foreign liver had acted as a kind of teacher, educating the recipient's immune system to behave friendly towards the transplanted organs. Once taught, the immune system remembered the lesson, no longer attacking them even after the teacher was gone.
The liver is the body’s largest internal organ, long thought to be mainly a metabolic workhorse, filtering blood and breaking down toxins. But Calne’s findings, along with work by later researchers, revealed that the liver also plays a vital role in immune regulation. It receives blood directly from the gut via the portal vein, constantly exposed to food particles, gut microbial fragments, and other foreign substances. Yet, not all of these are dangerous. So the liver takes on the job of educating the immune system, guiding circulating immune cells, teaching them not to overreact to harmless stimuli, but to focus their firepower on real threats.
Today, scientists like Jeffrey A. Hubbell, a bioengineer at the University of Chicago, are exploring how to harness this unique immune-taming capacity of the liver. And their goal: to retrain rogue immune cells, the ones that mistakenly attack our own healthy tissues, using the liver’s wisdom as a teacher.
Reverse Vaccines
The immune system is like an elite military force within our bodies. When pathogens invade or cells become cancerous, it springs into action, neutralizing the threat with precision. But even the most powerful army needs to know when to strike and when to stand down. If the immune system loses the ability to distinguish friend from foe, it may start attacking the body’s own cells, giving rise to a class of disorders known as autoimmune diseases.
Under normal circumstances, the immune system coexists peacefully with our own tissues, maintaining a careful balance. But that balance can be disrupted under certain conditions. Some people are genetically predisposed to autoimmune conditions, and environmental triggers also play a role. Viral infections, for instance, can sometimes set off autoimmune reactions. One line of evidence suggests that the Epstein–Barr virus (EBV) may be a trigger for multiple sclerosis (MS). Although the exact mechanisms remain unclear, researchers suspect that certain molecules on EBV resemble those in the human body. As a result, when the immune system targets the virus, it may also mistakenly attack the myelin sheaths that insulate neurons in the brain and spinal cord.
MS is just one example. Type 1 diabetes, celiac disease, rheumatoid arthritis, and systemic lupus erythematosus are also common autoimmune disorders. In developed countries, they affect an estimated 5 to 10 percent of the population, and rates are rising in developing countries as well. Patients often endure chronic pain, disability, and in some cases, life-threatening complications.
To control these diseases, many patients rely on long-term or even lifelong treatment with immunosuppressants. One of the most widely used drugs is adalimumab (also known as Humira), marketed by AbbVie. It works by blocking inflammatory factors, thereby damping down the immune response. With so many patients worldwide, Humira and similar drugs have become some of the top-selling medications on the global market. By broadly cooling down the immune system, these drugs can reduce its attacks on healthy tissues and help ease symptoms effectively.
But there’s a trade-off. Immunosuppressants do not cure autoimmune disease, they only offer temporary relief. When the drugs are stopped, the immune system quickly reactivates, often resuming its assault on the body. Worse, because these drugs suppress the immune system as a whole, they not only suppress immune responses to self-antigens, but also weaken its ability to defend against foreign antigens. Long-term users face an increased risk of infections and even cancer. In essence, these treatments flip the master switch, shutting down the body’s entire defense network, rather than fixing the specific part in the immune system that went haywire.
That’s partly because many of today’s immunosuppressants were originally developed not for autoimmune diseases, but for organ transplants or cancers like lymphoma, which involve malfunctioning immune cells. According to Lawrence Steinman, a neuroimmunologist at Stanford University, drug development often follows the safest and most well-trodden paths. In autoimmune research, that usually means repurposing existing drugs that have already been approved. Only a few researchers have dared to explore a more unconventional route: antigen-specific tolerance therapy. The idea is to retrain the immune system with pinpoint precision, teaching it to tolerate the very self-antigens it mistakenly targets.
In 2010, Steinman introduced the concept of reverse vaccines. Traditional vaccines teach the immune system to recognize and label invaders as enemies by exposing it to weakened or inactivated pathogens, or to fragments of the invaders. When the real, harmful pathogen shows up, the immune system is primed to respond swiftly and effectively. Reverse vaccines aim to do the opposite: rather than triggering an immune attack, they seek to induce selective forgetting, convincing the immune system to stand down when it encounters self-antigens.
“Vaccines are, by definition, antigen-specific,” explains Hubbell, “A flu vaccine won’t protect you from COVID. Likewise, a reverse vaccine designed for MS targets only the self-antigens involved in that condition. It doesn’t interfere with the immune system’s ability to fight off unrelated pathogens, which means fewer side effects.”
Beyond that specificity, reverse vaccines may offer another critical advantage: lasting immune memory. That would set them apart from conventional immunosuppressants. “Think of the tetanus vaccine,” says Hubbell, “A booster every ten years keeps you protected. That’s because your body remembers the immune training from the vaccine.” He hopes reverse vaccines can work in a similar way, requiring only a single dose every few years or even less frequently to provide long-term protection against autoimmune flare-ups.
A “Sweet” Vaccine
Hubbell’s lab has long focused on two seemingly opposite fronts: cancer and autoimmune disease. The two, in fact, are like two sides of the same coin. Cancer arises when abnormal cells manage to evade immune surveillance and escape destruction. Autoimmune diseases, by contrast, occur when normal cells lose their protected status and come under attack by the immune system. The key to fighting cancer is to break immune tolerance, while the key to treating autoimmune disease is to restore it.
In studying this delicate balance, Hubbell became intrigued by the liver’s unusual ability to suppress immune responses. He developed a reverse vaccine that could deliver self-antigens directly to the liver by chemically decorating them with sugar molecules.
The liver’s remarkable tolerance is closely tied to its unique cast of immune cells. Among them is a large group known as hepatic antigen-presenting cells, or HAPCs. Like other antigen-presenting cells (APCs), their job is to capture antigens and display them to naive T cells. Once activated, these T cells can kickstart a full-blown immune response.
But unlike many APCs that activate T cells, HAPCs tend to do the opposite: they suppress naive T cell activation. “In tissues like the mucosa, APCs usually trigger an immune response when they detect something foreign,” explains Shijie Cao, an assistant professor at Washington University who previously worked as a postdoctoral researcher in Hubbell’s lab. “But the liver has a naturally immunosuppressive environment.”
The liver is absolutely packed with HAPCs. These include specialized dendritic cells, Kupffer cells, hepatic stellate cells, and sinusoidal endothelial cells as well as the liver’s most abundant cell type, hepatocytes, which make up around 80 percent of this organ’s cells. When HAPCs present antigens to naive T cells, they can render those T cells inactive or even trigger their death. At the same time, they may coax the T cells into becoming regulatory T cells, the peacekeepers of the immune system, which can suppress other immune responses. In this way, the liver acts as a school for tolerance, retraining circulating immune cells that carry certain antigens here to behave in a less aggressive, more tolerant manner.
Hubbell’s idea was to exploit this capacity by guiding autoimmune-related self-antigens specifically into the liver’s immunosuppressive environment, in hopes of retraining the faulty immune cells that attack the body’s own tissues. He took inspiration from a natural process: every day, the body generates large numbers of apoptotic, or dying, cells. Their fragments circulate in the bloodstream, and most are quietly cleared by the liver without triggering an immune reaction. This gave him an idea: what if self-antigens could be disguised as apoptotic cell fragments and sent to the liver?
Apoptotic cell debris carries distinct sugar “tags” on its surface molecular signals that guide it towards the liver for clearance. “As cells undergo apoptosis,” Hubbell explains, “enzymes snip off the outer ends of the cell’s surface sugars, exposing inner sugar residues.” So Hubbell and his team decided to mimic that process: they chemically attached the same types of sugar molecules to self-antigens, disguising them as the remains of dying cells.
Once the glycosylated self-antigens enter the bloodstream, they are quickly taken up by the liver, where they induce antigen-specific immune tolerance. “Liver cells express high levels of a molecule called C-type lectin,” explains Cao. “This molecule binds to sugars, allowing the cells to internalize the antigens through endocytosis.”
By directing self-antigens specifically to the liver, this strategy not only promotes local immune tolerance within the organ but also has effects throughout the body. “One of the advantages of generating regulatory T cells is that they can circulate systemically,” says Hubbell. “When they encounter their target antigen in a particular tissue, they can locally suppress the immune response. In principle, we could attach these sugars to any antigen we want.”
In 2019, Hubbell’s lab demonstrated that glycosylated self-antigens could help prevent type 1 diabetes, an autoimmune disease in which the immune system attacks the insulin-producing beta cells of the pancreas. The researchers administered the reverse vaccine intravenously to mice during or shortly after the onset of diabetes-inducing conditions. Remarkably, the treated mice remained free of diabetes for an extended period.
“The liver plays a major role in shaping the immune system,” says Hubbell. “Its inner surface area is enormous, like a giant filtration device, so all sorts of molecules circulating in the blood pass through the liver first.” Based on this insight, and using glycosylated self-antigens as a delivery strategy, Hubbell co-founded Anokion, which aims to restore immune tolerance in patients with autoimmune diseases by targeting the liver. Two of the company’s candidate therapies are now in clinical trials.
But glycosylation isn’t the only way to steer self-antigens to the liver. For example, Stephen Miller, an immunologist at Northwestern University, and Lonnie Shea, a biomedical engineer at the University of Michigan, have taken a different approach: they encapsulate antigens in nanoparticles designed to be taken up by liver cells. This method is now being tested in a Phase II clinical trial by Takeda.
Other scientists have also turned to synthetic strategies to mimic the liver’s immunosuppressive function. At the University of Calgary in Canada, immunologist Pere Santamaria has engineered synthetic “tolerogenic antigen-presenting cells”. Like HAPCs, these materials can present antigens but lack the co-stimulatory signals needed to activate T cells. Santamaria calls them “T cell baits,” and has founded a biotech company called Parvus Therapeutics to develop this approach.
Other Paths to Reverse Vaccines
While many of the research on reverse vaccines has focused on the liver, scientists are also exploring other immune organs in the body. After all, the liver is not the immune system’s only school. Organs like the spleen, lungs, and lymph nodes are also home to abundant APCs that help determine the fate of T cells and other lymphocytes.
During his postdoctoral work in Hubbell’s lab, Cao focused on developing antigen-specific tolerance strategies that target the lymph nodes. And at the University of Maryland, immunoengineer Christopher Jewell is using polymer-based materials to deliver self-antigens directly to lymph nodes as a form of reverse vaccines.
For a reverse vaccine to work, immune cells need to encounter antigens in a “calm” environment. But lymph nodes are traditionally seen as hubs for immune activation, not tolerance. “Whether immune cells become activated really depends on the context in which they encounter the antigen,” Cao explains. For example, many conventional vaccines contain adjuvants, ingredients that stimulate a stronger immune response. That’s because injecting the antigens alone is often not enough to provoke a meaningful reaction.
“What’s more,” Cao adds, “self-antigens aren’t very immunogenic to begin with. And once you wrap them in a sugar coating, they become even less likely to activate the immune system.” In the absence of activating signals, exposure to these sugar-modified antigens tends to promote tolerance rather than immunity. Still, Cao notes that the optimal tissue target for a reverse vaccine may depend on the specific disease and how the treatment is administered.
And some scientists are exploring a different approach to reverse vaccines: instead of delivering self-antigens directly, they deliver the genes that encode them. Steinman, who first proposed the concept of reverse vaccines, began experimenting with DNA-based inverse vaccines for autoimmune diseases as early as the 1990s. He also founded biotech companies such as Bayhill and Pasithea to develop this strategy.
Even BioNTech, the company that rose to global prominence for its rapid development of mRNA vaccines during the COVID pandemic, is now working on mRNA-based vaccines for autoimmune disorders. Nykode Therapeutics has gone a step further: its DNA-based reverse vaccines encode proteins that not only target suppressive APCs, but also include anti-inflammatory immune modulators, aiming to combine precise delivery with active immunoregulation.
In animal models, these reverse vaccines have already shown promise for preventing autoimmune diseases. In 2022, Pasithea reported that its DNA vaccine PAS002 prevented MS in about 50% of mice. It delayed the onset of tail paralysis, reduced disease severity, and lowered the relapse rate. mRNA vaccines developed by BioNTech and two DNA-based candidates from Nykode have demonstrated similarly encouraging results.
Still, Hubbell points out that using non-biodegradable polymers to deliver self-antigens or the genes that encode them could pose safety concerns. Cao noted that for clinical use, researchers may need to focus on systems that are simpler, safer, and more readily translatable to human. One promising direction, he suggests, may be to return to more straightforward strategies, such as chemically modifying the antigens.
Hope and Hurdles
While reverse vaccines have shown great promise in preclinical studies for preventing autoimmune diseases, the more urgent challenge in the real world is treating them. As Hubbell explains, prevention and treatment are fundamentally different. In prevention, the goal is to influence naive T cells, those that have not yet reacted to self-antigens. But in patients with established autoimmune disease, the immune system already contains memory cells that have been trained to attack. Upon re-encountering self-antigens, these cells can launch a rapid and aggressive response. As a result, strategies that work in prevention may not succeed in treatment.
Surprisingly, however, glycosylated self-antigens are beginning to show therapeutic potential. In mouse models of experimental autoimmune encephalomyelitis (EAE), a disease similar to MS, Hubbell’s team found that reverse vaccines significantly reduced disease severity. Even more strikingly, after a period of treatment, the animals not only avoided relapse but showed steady improvement. In nonhuman primate models, the vaccine was also able to reverse an already established immune response. These results, published in Nature Biomedical Engineering in September 2023, drew widespread attention. “Before this, hardly anyone had managed to reestablish immune tolerance in the presence of preexisting immune memory,” says Hubbell.
In 2024, Anokion released early clinical data from its two reverse vaccine candidates. In a Phase Ib/II trial, KAN-101, designed for celiac disease, induced biomarker changes in patients that were consistent with immune tolerance, including shifts in cytokine levels and immune cell activity. Meanwhile, ANK-700, developed for relapsing-remitting MS, demonstrated good safety and biological activity in a Phase I trial. That same October, Parvus Therapeutics also launched a first-in-human clinical trial to test its reverse vaccine for primary biliary cholangitis, a chronic autoimmune liver disease.
Despite early signs of success in clinical trials, Hubbell remains cautious. “We did observe some biomarkers in patients that suggest the therapy is working,” he says, “but to fully evaluate its efficacy, we still need larger, later-stage clinical trials.” Over the past few decades, many strategies aimed at inducing antigen-specific immune tolerance have shown promise in animal models, but none has yet led to an approved drug.
The path from animal studies to regulatory approval is often long and difficult. One major reason for inverse vaccines is that suitable animal models are lacking for many autoimmune diseases. In the case of MS, researchers use EAE in mice as a stand-in. Although the mouse genome shares similarities with that of human, important differences remain. And among nonhuman primates, whose immune systems more closely resemble our own, there are currently no models for autoimmune diseases. This presents a significant hurdle. In their own primate studies, Hubbell’s team had to first vaccinate primates with simian immunodeficiency virus to establish an immune response, then test whether the reverse vaccine could retrain it.
Another open question is how long the effects of a reverse vaccine will last. After all, even traditional vaccines can lose effectiveness over time. Steinman notes that preclinical data suggest PAS002 may require periodic dosing. Deborah Geraghty, CEO of Anokion, adds that future reverse vaccines may need to be administered in a regimen that starts with a priming dose, followed by occasional boosters to help keep the immune system on track.
Another major challenge for reverse vaccines lies in selecting the right antigens. For autoimmune diseases like rheumatoid arthritis and psoriasis, scientists still don’t fully understand which self-antigens play a dominant role. Moreover, most autoimmune diseases involve multiple antigens. As the disease progresses, chronic inflammation can cause the immune system to start recognizing and attacking additional self-antigens beyond the one that triggered the initial response. This means a reverse vaccine designed to target just one antigen may not be sufficient to treat the disease effectively. Complicating things further, the relevant antigens can vary from person to person, so a one-size-fits-all vaccine might not work for every patient.
However, Geraghty notes that in Phase I trials, researchers observed signs of immune tolerance not only to the antigens included in the reverse vaccine, but also to other self-antigens. This effect may be due to the generation of regulatory T cells, which can help suppress a broader autoimmune response.
An even more pressing concern is whether injecting self-antigens into patients who already have strong immune responses against them might worsen the disease, especially when using DNA or mRNA vaccines. Foreign DNA and RNA molecules are typically flagged by the immune system as dangerous, triggering immune responses. To address this issue, both BioNTech and Pasithea Therapeutics have specially engineered their nucleic acid-based vaccines. By modifying highly immunogenic nucleotides, they aim to reduce the likelihood that these vaccines will provoke unintended immune activation.
Beyond Autoimmune Disease
But the potential of reverse vaccines may extend well beyond autoimmune disorders, because many health problems stem from an overactive immune response. One of them is allergy, a condition that Cao has long focused on, especially the rising concern of food allergies.
The standard treatment for food allergies today is oral immunotherapy (OIT), which involves giving patients gradually increasing doses of an allergen to train the immune system to tolerate it. But the success rate is modest, and patients must often undergo long, repeated treatments to maintain desensitization. The process can also cause gastrointestinal side effects, which reduce patient compliance. Cao hopes to develop a new approach that works faster and causes fewer side effects.
He believes that glycosylated reverse vaccines could offer just such a solution. Allergic reactions occur when the immune system mistakenly identifies harmless antigens as dangerous. This prompts plasma cells to produce allergen-specific IgE antibodies, which then trigger inflammation. T cells play a crucial role in helping B cells mature into these plasma cells. By targeting APCs, a glycosylated reverse vaccine could intervene early in this chain of events, ultimately modulating downstream B cell responses and preventing the allergic reaction.
For patients with food allergies, directly injecting allergens into the bloodstream carries serious risks. To meet the demands of safety and clinical translation, Cao chose to test subcutaneous delivery of reverse vaccines. When glycosylated allergens are injected under the skin, they diffuse into nearby lymphatic vessels and eventually reach the lymph nodes. There, APCs that express C-type lectins take up and present the allergens, helping to induce antigen-specific immune tolerance.
In a study published in Cell Reports Medicine in January 2024, Cao and his colleagues showed that reverse vaccines could effectively prevent milk allergy in animal models. Mice that received glycosylated milk antigens no longer exhibited severe allergic reactions to milk. Hubbell adds that his lab is also collaborating with Melody Swartz, a professor at the University of Chicago, to explore whether reverse vaccines can help treat allergic asthma.
Still, using reverse vaccines to treat established allergies remains a significant challenge. “T cells can influence the early stages of B cells differentiation,” explains Hubbell, “but once B cells have matured into antibody-secreting plasma cells, they can continue producing antibodies without T cells’ help.” That means reverse vaccines may be less effective in such diseases driven primarily by B cells. Cao agrees that fully reversing the immune memory of allergy will likely require deeper insights into how reverse vaccines affect B cells or combining inverse vaccines with additional immunomodulatory strategies.
Beyond autoimmune diseases and allergies, reverse vaccines could also impact the use of biologic therapies, such as antibody drugs and cell therapies. Compared with small-molecule drugs, biologics are larger in size and often produced in microbial systems, making them more likely to be flagged by the immune system as foreign. In some patients, this immune recognition leads to the production of anti-drug antibodies (ADAs), which can reduce the drug’s effectiveness, cause side effects, or even endanger the patient’s life.
Research from Hubbell’s lab suggests that reverse vaccines could help prevent this anti-drug immune response. In animal studies, pre-treatment with a reverse vaccine targeting a specific biologic induced antigen-specific tolerance and significantly reduced the formation of ADAs. As a result, the biologic remained active in the body for a longer time, rather than being rapidly cleared. According to Hubbell, this approach could be applied broadly to enhance the effectiveness of many types of biologics.
Reverse vaccines may also find a role in the field where Calne once made his mark: organ transplantation. Early in his career, Calne dedicated himself to developing drugs that could suppress the immune system and reduce transplant rejection. In the 1960s, he was the first to demonstrate the immunosuppressive power of azathioprine, and later helped introduce cyclosporine into transplant medicine, a breakthrough that laid the foundation for modern transplantation. Today, cyclosporine remains widely used to prolong graft survival and improve outcomes for transplant recipients. In recognition of these pioneering contributions, Calne was awarded the Lasker Award in 2012.
In the realm of organ transplantation, Hubbell’s team has now taken the concept of reverse vaccines one step further. In a mouse model of skin transplantation, they found that when animals were pretreated with a reverse vaccine containing glycosylated antigens derived from donor skin, the immune rejection that usually follows transplantation could be significantly delayed, or even prevented altogether. If this strategy proves effective in human organ transplants, it could one day spare patients the lifelong burden of broad-spectrum immunosuppressants and their serious side effects.
From autoimmune disease to allergy, anti-drug immune reactions, and now transplantation, the potential of reverse vaccines is steadily coming into view across a wide swath of medicine. According to Geraghty, in addition to targeting celiac disease, MS, and type 1 diabetes, Anokion is exploring the use of reverse vaccines in larger-market conditions such as rheumatoid arthritis and Crohn’s disease. Meanwhile, Hubbell’s team is also developing a candidate for neuromyelitis optica, a rare autoimmune disorder that affects the spinal cord and optic nerves. One preclinical study after another along with early clinical trials has begun to reveal the unique promise of reverse vaccines in both preventing and treating immune-related disease, offering new hope to patients with few remaining options.
Reverse vaccines may open an entirely new chapter in medicine, perhaps not only transforms our understanding of the immune system, but also redefines how we treat immune-related diseases. In the not-so-distant future, immunity may become a partner that scientists can precisely retrain. These emerging therapies are quietly sketching the contours of a future rich with possibility, one in which we treat disease more wisely, and rewrite the destinies of millions.
