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hen a leaf of poison ivy brushes someone’s skin for the first time, it leaves no visible trace. There’s no rash, and the skin doesn’t itch. But inside the body, the lick of uru-shiol oil from the plant’s sap awakens the immune system, causing T cells, a type of

immune cell, to surface on the skin and form a deep immuno-logical memory of the oil. The next time that person encoun-ters poison ivy, the immune system recognizes it quickly, and within 24 hours the skin erupts in a rash and bursting pustules. In this case, the response is an allergic overreaction to the uru-shiol oil and the skin proteins it altered as it penetrated the skin, which the immune system cells then recognize as foreign and work to eliminate. The same kind of reaction, in other cir-cumstances, could ward off a dangerous infection.

For years, scientists have understood that the body’s adap-tive immune system engineers this intense response the sec-ond (or perhaps third or fourth) time a foreign substance is encountered. Conventional wisdom has held that only adap-tive immunity, armed with T cells and B cells, possessed the complex biological machinery to remember a particular for-eign molecule or microbe and to mount a vigorous immune response. Vaccines are predicated on this notion.

A second, more primal mode of infection fighting—the in-nate immune system—differs in that it begins working the moment a foreign substance enters the body. It is the body’s brutish first line of defense, recognizing common features that distinguish microbes from ourselves, and it quickly kills

by rachael moeller gorman // IllustratIons by mIcah lIdberg

not just brute force:Innate immunity kicks in the moment a foreign substance invades // Kills generic physical structures // but also employs what it was never thought to have: a memory

Our Innate Defense

the invaders. But innate immunity works on generalizations, with its cells—including natural killer (NK) cells and phago-cytes—and proteins systematically making their way through the body on the hunt for generic physical structures typical of microbes but not of humans. Still, these crude search-and- destroy missions can’t eliminate every type of virus or bacteria, as some have evolved to avoid attack; Staphylococcus bacteria, for example, produce an enzyme that breaks down the chemi-cals phagocytes use to kill those germs. Nor is the innate im-mune system powerful enough to kill every invader. But the biggest difference between innate and adaptive immunity was always thought to be the innate immune system’s inability to remember—and thus to attack with immediate, precisely tar-geted power—a microbe it has encountered before.

Because of all those apparent deficiencies, the innate im-mune system has never gotten much respect or attention as a vehicle for disease treatment or drug development. Innate immunity’s perceived shortcomings were also why the results of the experiments Ulrich von Andrian began conducting in 2002 were so shocking. Von Andrian, Mallinckrodt Professor of Immunopathology at Harvard Medical School, was looking at contact hypersensitivity (a laboratory version of a brush with poison ivy) in the bladders of mice. In a standard control exper-iment, von Andrian’s team used animals called RAG2-deficient mice, which lacked T cells and B cells—in other words, they had no adaptive immune system. They were protected only by blunt-edged, slash-and-burn innate immunity, which shouldn’t have been able to remember a thing.

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But when the team re-exposed these RAG2-deficient mice to a foreign invader, a chemical they had encountered before, the altered mice responded with just as much infection-fighting inflammation as mice whose adaptive immune systems were intact. “It was an experiment that initially seemed to have gone awfully wrong,” says von Andrian, who assumed the team had made mistakes. “Certainly it was not explainable with any of the expert knowledge broadly accepted at the time.” Yet af-ter years of additional work, von Andrian published a paper in 2006 reporting that the innate immune system—in particular, a subset of its NK cells—can indeed remember.

Many immunologists didn’t believe it, especially because von Andrian couldn’t explain how NK cells, with none of the adap-tive immune system’s T cells and B cells, could possibly remem-ber an attacker. Other scientists were astonished; in one news report, a researcher was quoted as saying “it’s like Christopher Columbus bumping into a new continent.” But along with other recent discoveries about innate immunity, von Andrian’s work is helping change the way science looks at the innate im-mune system, suggesting that it may be fighting more battles than anyone had imagined—and that it could be uniquely use-ful in efforts to attack HIV/AIDS, asthma and other diseases.

W hen life emerged several billion years ago, single-cell organisms had only a thin membrane sepa-rating them from their turbid watery surround-

ings and the organisms that wanted to engulf them. But as multicellular organisms evolved, so did a coherent immune system. This first appeared some 600 million years ago with the emergence of sponges, which possess immune molecules. Other, more advanced invertebrates, such as insects, worms and clams, later recruited additional proteins and cells to fight invaders. Vertebrates also have this innate immune system.

Scientists theorize that adaptive immunity, with its power-ful T cells and B cells, came along about 500 million years ago, showing up first in a common ancestor of jawed vertebrates. Adaptive immunity gets its bite through a process called VDJ recombination. The body has many different gene segments that must be brought together to code for the parts of antibod-ies or T cell receptors that recognize foreign substances, and they’re divided into three categories: V (variable), D (diversity) and J (joining). An enzyme called VDJ recombinase randomly splices together one of several hundred V gene parts with one of several different J and D parts. Those spliced parts, along with many additional DNA sequences added along the way, produce genes that code for unique binding sites for antibodies (produced within B cells) or T cell receptors, and they can bind

to and instigate destruction of an almost infinite array of whole or partial microbes.

Antibodies produced by B cells attack microbes in the blood and other body fluids, while T cell receptors seek out and de-stroy infected cells. The body reserves some of these special-ized B cells and T cells to mount a fast, powerful assault should the same invader show up again. Creatures with adaptive im-munity have a strong selective advantage over those with only innate immunity, and so they thrived, making adaptive immu-nity ever more prevalent in all higher-level vertebrates.

Most immune system research has been focused on adaptive immunity, and much of modern medicine is based on antibod-ies. Most vaccines introduce harmless pieces or inactivated versions of a foreign microbe into the body to stimulate an adaptive immune response in case the person vaccinated ever encounters the real version. Yet there’s a twist to that approach, necessitated by the observation several years ago that certain batches of a vaccine often worked significantly better than another batch did. Scientists eventually discovered that effec-tiveness was related to how clean the manufacturing containers were—and that dirtier containers somehow helped boost the immune response. To achieve that desired result more system-atically, “adjuvants” laced with bacteria or alum were added.

T he immunology landscape began to shift toward a great-er appreciation of innate immunity’s role after Yale Uni-versity immunologist Charles Janeway Jr. introduced his

landmark 1989 paper at the Cold Spring Harbor Symposia on Quantitative Biology. Janeway asserted that the innate immune system works with the adaptive immune system, turning it on

Scientists are realizing that adding compounds that stimulate particular TLrs can increase a vaccine’s effectiveness well beyond the improvement it might get from other adjuvants.

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S ome of the most advanced recent work on innate im-munity involves asthma. The airways of asthmatics are “hyperresponsive” to any inhaled allergen, resulting in

inflammation that can be severe and impede breathing. The inflammation seems to be the fault of T-helper 2 cells (Th2), a type of adaptive immune system T cell associated with al-lergic disorders. Asthmatics appear to have more than their share of these highly inflammatory Th2 cells—and the immune cells and proteins that Th2 cells direct—and relatively fewer T-helper 1 cells, which are involved in a much milder immune re-sponse. If there were a way to switch asthmatics’ Th2-mediated immune response over to a lower-level Th1 response, it might be possible to treat the disease at its roots—by heading off the immune system overreaction that causes asthma in the first place—instead of simply addressing its symptoms with cortico-steroids and bronchodilators that treat inflammation and allow asthmatics to breathe freely.

It turns out that the innate immune system helps turn on the T-helper response. TLR9, an innate-immune-system PRR produced in airway cells, activates the Th1 part of the adaptive immune system, and scientists have found that turning it on with a drug reduces inflammation in mice, decreasing the al-lergic Th2 response and increasing the Th1 response.

like a light switch. Among several new theories that Janeway proposed, the most important was that innate immune cells possess pattern-recognition receptors (PRRs) that can recog-nize generic sets of proteins or gene code that are unique to foreign microbes. PRRs initially trigger an innate immune re-sponse. But when activated, Janeway suggested, they also send a “second signal” to the adaptive immune system, informing it that a “non-self ” entity has been encountered and providing a general idea of what kind of microbe it’s dealing with. Janeway proposed that this interaction helps ramp up the adaptive im-mune system and guides its response. That would explain why vaccines need adjuvants to engage their immunological mem-ory—because PRRs are provoked by the adjuvants to put adap-tive immunity on high alert. In invertebrates that lack adaptive immunity, PRRs are sufficient to recognize invading microbes and marshal the forces of innate immunity against them.

During the next several years, Janeway’s hypotheses bore experimental fruit. In 1997, Janeway and Ruslan Medzhitov (also at Yale) discovered that a human cousin of Toll—an an-tifungal protein in fruit flies—called the Toll-like re-ceptor (TLR) was involved in innate immunity. They proposed that TLR was a type of PRR, a notion later confirmed by other research. Scientists have since identified 10 human TLRs. Found on many cells of the innate immune system, each TLR recognizes a differ-ent microbial pattern—a flagella tail protein on a bac-terium, for example—that triggers inflammation or killing by another cell of the innate immune system.

The most exciting thing about TLRs, however, is how useful they are in creating vaccines. Scientists are realizing that adding compounds that stimulate par-ticular TLRs can increase a vaccine’s effectiveness well beyond the improvement it might get from more gen-eralized adjuvants. The Food and Drug Administra-tion has approved a vaccine for human papillomavi-rus that stimulates TLR4, one of the 10 human TLRs, while the European Union has approved a hepatitis B virus vaccine that stimulates TLR4. The addition of the TLR means that patients require fewer vaccine doses, and the improved, more targeted vaccines also work better in immunocompromised people, whose restrained immune systems often respond poorly to other vaccines.

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The prevalence of asthma has increased during the past few decades, a phenomenon that might be explained by the “hy-giene hypothesis”—the idea that reduced exposure to patho-gens in childhood may boost the risk of developing asthma later on. That notion is supported by research showing that children living on farms, where they encounter high levels of the allergen endotoxin, a component of the bacterial cell wall, are less likely to have asthma. Scientists think TLR9 could play a role here too, and that stimulating TLR9 with a drug could mimic this sort of infectious exposure in city-dwelling kids, cutting their chance of asthma. One company, Dynavax Technologies, has developed an asthma drug targeting TLR9 that is just beginning clinical trials.

Other recent research involves Crohn’s disease, a disorder marked by intense intestinal inflammation thought to be caused by T cell–driven inflammation in response to generally harmless bacteria in the gut. Until now, most Crohn’s treatments have focused on suppressing the entire immune system. The new work centers on a type of PRR called NOD2 (nucleotide-binding oligomerization domain containing protein 2) that recognizes a component of the bacterial cell wall. Normally, NOD2 sparks a modulated response to the bacteria. But if the NOD2 gene con-tains one or more mutations, Crohn’s disease is likely to result, because of inflammation triggered by the gut microbes.

To treat Crohn’s, gastroenterologist Joshua Korzenik at Brigham and Women’s Hospital in Boston has taken a seemingly counterintuitive approach, giving patients a drug that, rather than dampening the immune system, increases the number and function of certain innate immune cells. In a 12-week trial, 55% of Crohn’s disease patients who got the medication had reduced symptoms, and one in four achieved longer-lasting relief from the debilitating disease.

I n 2010, von Andrian and his team published a paper in Nature Immunology demonstrating that NK cells in the liver not only remember the brush of a chemical on the

skin but also recall encounters with viruses that harm or kill humans, including influenza and HIV. When NK cells from

Filtering Out HIV //scientists looking to block hIV’s evasions of the immune system found an unlikely source of inspiration: the spam filter.

In the early days of e-mail, spammers went unchecked, sending scores of unwanted messages to unsuspecting in boxes. But in 1997, computer scientist David Heckerman and colleagues at Microsoft began creating ways to stop this flood of junk mail; the spam filter was born. Spammers soon realized their messages were being fended off, however, and altered e-mails to avoid detection. Heckerman just as quickly adapted his algorithm, forcing spammers to make still more changes, and so on. Because spam’s objective is to coax people to go to Websites and enter credit card numbers, Heckerman’s team compiled a continually updated list of spammers’ Websites and created an algorithm to scan e-mail for links to those sites and to remove junk messages before they reached in boxes. Heckerman says this tug-of-war is similar to what happens between a virus such as HIV and the human immune system. “Spammers mutate their message to work around the spam filters, and HIV mutates to avoid attack by our immune system,” he says.

Heckerman, who also is trained as a physician, went on to direct the eScience Research Group at Microsoft Research, where he developed probability models to examine how HIV evolved under certain evolutionary pressures. One model, PhyloD, helps find regions of the virus’s DNA that are mutating, most likely as a result of pressures from the immune system. PhyloD examines HIV one amino acid at a time, determining whether a patient’s immune system causes an amino acid to change at a given position, thus creating a hole for the “spam” to slip through the “filter.”

Some 30 scientific papers have resulted from Heckerman’s academic collaborations. Scientists may one day use such information to create a resistance-proof vaccine—the ultimate spam filter.

VIDeO: More on Heckerman’s HIV model and how Massachusetts General Hospital vaccine researchers are using it

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mice vaccinated against these viruses were transferred to un-vaccinated mice, the unvaccinated mice were also protected. All told, von Andrian found, NK cells could remember and dis-tinguish among at least five different antigens (he has studied only five so far), and that a particular receptor on the NK cells, CXCR6, was the key to this ability.

A commentary by immunologist Christine Biron called the paper “highly significant, maybe even revolutionary,” es-pecially because it suggested that NK cells could become a target for vaccine developers (although no one has been able to explain how NK cells remember). It’s true that NK cells lack adaptive immunity’s memory machinery, but von Andrian suspects they possess some other mechanism that allows them to rearrange their genes in an almost infinite number of ways, and he’s working with several research groups to find that missing link.

Scientists have yet to show whether human NK cells, like those in mice, can remember an antigen. But if that proves to be the case, it could spur vaccine development—perhaps even for HIV. Scientists have known for some time that human NK cells can kill HIV-infected cells in the lab, but until recently it wasn’t clear whether NK cells also helped control HIV in hu-mans. For a study published in Nature in 2011, Massachusetts General Hospital scientist Marcus Altfeld came up with an el-egant way to find out. He theorized that if NK cells indeed go after the HIV virus, they should eventually force the virus to evolve in a way that thwarts attack.

Working with MGH virologist Todd Allen, Altfeld’s labora-tory sequenced the RNA inside the HIV virus from 91 people to document any variations in the code. Then, working with a group from Microsoft, the MGH group compared the varia-tions they found with receptors of NK cells from the same patients. They discovered that patients who possess NK cells with a receptor called KIR2DL2 tend to have a particular set of HIV mutations that somehow keeps the NK cell from killing the virus. “To persist,” Altfeld says, “the virus is actually forced to adapt to its host.” The new HIV mutations allowed the virus to hide, survive and thrive.

The work suggests that it might be possible to harness NK cells to treat HIV. If some NK cells in humans turn out to have immunological memory, it’s possible that they could be used in a vaccine. “The advantage of NK cell memory compared with T cell memory is that NK cells are even quicker than T cells to respond to the incoming virus,” Altfeld says. “And we know that we have only a very limited number of days during which we can protect someone completely from HIV infection.”

The intriguing possibility that NK cells could aid in finally developing an HIV/AIDS vaccine is just one more example of the innate immune system’s moving to center stage in immu-nological research. It could even suggest that old views about innate and adaptive immunity may have to change in a very basic way—that instead of a two-part, memory/nonmemory system, “what we have always understood to be divided be-tween adaptive and innate immunity may have to be reimag-ined as a trinity,” von Andrian says. NK cells, with their ability to remember the microbes they’ve encountered before, may eventually be recognized as a third, uniquely useful arm of human immunity.

DOSSIeR1. “t cell– and b cell–Independent adaptive Immunity mediated

by natural Killer cells,” by jacqueline o’leary et al., Nature Immunology, may 2006. the controversial study in which immunologist ulrich von andrian demonstrates that at least one component of the innate immune system, natural killer cells from the liver, can remember foreign substances they previously encountered—overturning a fundamental rule of immunology.

2. “hIV-1 adaptation to nK-cell-mediated Immune Pressure,” by galit alter et al., Nature, aug. 4, 2011. a demonstration of the fact that natural killer cells play a powerful role in fighting hIV, which, taken together with von andrian’s paper, allows scientists to theorize that vaccines might be developed that target nK cells in addition to the traditional cells of adaptive immunity.

3. “approaching the asymptote? evolution and revolution in Immunology,” by charles janeway jr., Cold Spring Harbor Symposia on Quantitative Biology, 1989. janeway’s theories on innate immunity, presented here, marked the first time the innate immune system was recognized as a powerful defensive system in its own right; all of janeway’s theories eventually proved true.

Scientists have yet to show whether human natural killer cells can remember an antigen. But if that proves to be the case, it could spur vaccine development.