About a Virus
By Jason Socrates Bardi
first [precept] was never to accept anything for true which I did not
clearly know to be such; that is to say, carefully to avoid precipitancy
and prejudice, and to comprise nothing more in my judgement than what
was presented to my mind so clearly and distinctly as to exclude all
ground of doubt."
Descartes, Discourse on the Method of Rightly Conducting the Reason,
and Seeking Truth in the Sciences, 1638
It is the early 1970s and a nurse named Johnny accidentally sticks himself
with a needle while doing a routine blood draw, exposing himself to the
hepatitis B virus (HBV). There are at this time no screens for the virus,
and aside from admonishing himself for his clumsiness and washing the
tiny wound with antibiotic soap, Johnny thinks nothing of it.
A few weeks later, while the virus is replicating prolifically in his
liver, he transmits hepatitis B to his wife during intercourse. Unbeknownst
to either of them, she is already pregnant. And when their baby is born,
he is also infected.
The odds, in this fictionalized case, are that Johnny and his wife both
fully recover from their infection. Their immune systems mount a strong
defense against the virus and it is eliminated from their systems. The
odds do not favor their son, however. His immature immune system will
most likely not be able to fight off the hepatitis B virus, and it will
establish a chronic, lifelong infection in his liver. Like all other chronically
infected people, he will have potentially lethal health problems and an
enormously increased risk of developing liver cancer.
In the United States, there are 1,250,000 people living with chronic
hepatitis B, according to the Centers for Disease Control and Prevention
(CDC). The average Americans lifetime chances of being infected
by HBV are about five percent, and about five percent of those infections
will become chronic.
Globally, the situation is more dire. Nearly half the worlds population
lives in areas where more than eight percent of people are chronically
infected by hepatitis B. Anyone living in those areas has a greater than
60 percent chance of being infected by hepatitis B virus at some point
in their lifetime. Hepatitis B is the leading cause of liver cancer in
There are 350 million people in the world who are chronically
infected with hepatitis B, says physician Frank Chisari, who is
professor in The Scripps Research Institute (TSRI) Department of Molecular
and Experimental Medicine.
My lifelong dream is to contribute to the termination of hepatitis
B infection in all those chronically infected peoplethat has been
driving my research throughout my career.
Cells Can Cure Themselves
Hearing of goals, rather than of accomplishments, is strange from someone
who has recently received more than one lifetime achievement award.
A few weeks ago, Chisari and TSRI Chemistry Professor Chi-Huey Wong
were elected to the National Academy of Sciences, becoming two of the
now 14 investigators at TSRI who have been admitted to this august body.
And just days ago, he was elected to the American Academy of Microbiology,
the highest honor the American Society of Microbiology bestows upon its
members. Both honors recognize the work Chisari has done on hepatitis
since coming to TSRI in 1973.
In the last three decades, by studying infections in patients and in
a closely related species, and by developing transgenic models to study
the HBV immunobiology and pathogenesis, Chisari and his collaborators
have characterized the course of HBV infection in the liver, the immune
systems response to the virus, and the mechanisms whereby a chronic
HBV infection can lead to liver cancer. In recent years, he and his collaborators
completed a comprehensive analysis of the virological and immunological
features of HBV infection using liver biopsies and blood samples they
obtained from infected subjects every week for six months after inoculation,
describing the course of infection with a level of detail that had never
before been attempted.
The insights they gained from these studies and their earlier human
and transgenic model experiments have revolutionized the way we think
the immune system can control a viral infection. Furthermore, they also
demonstrated that theres a dark side to the antiviral immune response,
which can produce progressive tissue damage and even trigger the development
of cancer when it goes awry.
Hepatitis is caused by one of several evolutionarily distinct viruses
(called A, B, C, D and E) that all target hepatocytes, the parenchymal
cells of the liver. Hepatocytes are the tiny chemical factories in the
liver that produce most of the proteins present in blood, nurturing all
the other organs of the body. They also produce bile, a fluid used for
digestion of fat in the diet and for the elimination of waste.
Hepatitis B virus is a circular, double-stranded DNA virus just over
3,000 base pairs long belonging to the Hepadnaviridae family. The
infectious particle, or virion, contains this tiny genome and a viral
polymerase enzyme in a protein capsid shell surrounded by a lipid coat.
HBV infection starts when these virions are introduced into the bloodstream
through routes that are similar to those used by the human immunodeficiency
virus (HIV)unprotected sex, contaminated needles, and mother-infant
Once inside the bloodstream, the virions eventually pass through the
liver, and the process of disease starts when HBV infects one or more
liver hepatocytes. The initial number of cells infected may be smalljust
a fewbut within six to eight weeks, the virus rapidly replicates
and can infect every hepatocyte cell in the liver.
Upon reaching this widespread infection, there is a rapid spike of viral
DNA in the bloodstream and the initiation of an immune response, which
is evident by the appearance of T cells in the liver and a reduction by
several orders of magnitude in the amount of virus in the blood.
Most adults who are infected with hepatitis B suffer an acute infection.
After the HBV activity peaks, the body mounts an immune response and the
virus disappears. The immune response is so effective that the liver goes
from having all its hepatocytes infected to having none of them infected.
Over a decade ago, Chisari suspected that the immune system must be
using an unexpected way of clearing the virus from infected liver cells
during an HBV infection, because in many cases it was clearing the virus
without killing off all the infected cells.
For years, scientists had recognized that one of the principal ways
that the immune system deals with a viral infection like HBV is to unleash
cytotoxic T lymphocytes (CTL), also called killer T cells, which carry
a receptor on their surface that specifically recognizes tell-tale viral
markers on the surface of infected cells that indicate these target
cells should be eliminated. CTLs then kill these infected cells by inducing
them to undergo apoptosis, the cellular equivalent of suicide. Until recently,
however, this destructive process was thought to be the only antiviral
mechanism that CTLs had at their disposal.
But Chisari realized that this couldnt be the primary mechanism
for clearing HBV because killing requires direct contact between a CTL
and an infected hepatocyte, and there are simply not enough killer T cells
to kill off every hepatocyte in the liver. And even if there were, killing
your liver is the last thing your body would want to do, because it is
impossible to live without this vital organ.
So, in the early 1990s he started looking into the possibility that
CTLs might be able to coax infected cells into curing themselves without
being destroyed. The mechanism of this clearance occupied nearly a decade
of Chisaris time, and a few years ago he and his colleague Luca
Guidotti, an Associate Professor at TSRI, demonstrated that the immune
system can indeed help cure infected cells and how this intracellular
effector function may actually be the primary way that the immune
system controls HBV infectionsomething that took most people by
This unprecedented concept established a new paradigm in our understanding
of the host-virus relationship, and like many revolutionary ideas, was
initially met with surprise and skepticism. In the past several years,
however, it was independently confirmed for HBV and it has been extended
to a number of other infections as well.
The Immune System Helps Cells that Help Themselves
Basically, in addition to the direct killing of infected hepatocytes,
the activated killer T cell will start to produce and secrete chemicals,
called cytokines, that bind to surrounding cells that are also infected
and that carry specific markers to which the cytokines bind.
Once these cytokines bind to an infected cell, that binding event activates
genes within the infected cell that produce proteins that intercept the
lifecycle of the pathogen, leading to an internal elimination of the virus
without destroying the cell. In hepatitis, the primary cytokine that drives
this processwhich also occurs in other cells that are infected with
other pathogensis called interferon-gamma (IFN-g).
In hepatitis, Chisari and Staff Scientist Stefan Wieland in his group
demonstrated that the first defense mechanism of INF-g involves interrupting
the assembly of the viral RNA and associated proteins into infectious
Assembly of [capsid] is very rapidly abolished by signals that
are delivered by IFN-g, says Chisari. In recent years, he has worked
to categorize the molecules that are produced by HBV-infected liver cells
after they are activated by IFN-g.
One candidate class he and his postdoctoral fellow Michael Robek have
found to be upregulated in response to the cytokines are proteins of the
proteasome, the cell organelle responsible for degrading protein in the
cells cytoplasm. Chisari has demonstrated that treating HBV-infected
cells with inhibitors of these proteasome proteins blocks the antiviral
activity of IFN-g.
Clearance is not limited to this one mechanism. A second, slower mechanism
that HBV-infected cells engage after they are turned on by IFN-g is to
remove all the viral RNA from the cell by destroying a cellular protein
that protects the viral RNA. Without the protection of this cellular protein,
the viral RNA is susceptible to ribonuclease enzymes in the cytosol, which
Nor is the production of cytokines during such an immune response limited
to one type of immune cell. Multiple cells of the immune system, including
cytotoxic T lymphocytes, helper T cells, natural killer cells, macrophages,
and dendritic cells all release such cytokines. And when these cells are
activated to produce IFN-g in the liver, the infection will be cleared.
We think this is what happens in most of the acute infections
in adult patients, says Chisari. [Cytokine-induced viral clearance]
is the dominant effector force for the control of HBV infection.
Not every intracellular event involved in this clearance is known, and
a large portion of Chisaris laboratory is busy mapping all the details.
Nevertheless, the usefulness of purging the infection while preserving
the integrity of the cells is obvious when one compares acutely infected
patients to the more serious, chronic cases: acute infections are rapidly
controlled by the immune system and chronic infections are not.
Chronic hepatitis is a smoldering infection, in which the
body fails to clear the virus from all the infected cells. What the body
does do, however, is to unleash its killer T cells in an attempt to clear
the infection. However, for reasons that are not entirely clear, the T
cell response isnt vigorous enough to eliminate the infection. Indeed,
the number of HBV-specific T cells produced by these patients is 100 to
1000 fold lower than in patients who clear the infection. This leads to
a slow, progressive process in which the outnumbered T cells are able
to kill some of the infected hepatocytes, but not enough of them to terminate
the infection of a large organ like the liver.
However, what they can do is continue killing... and that sets the stage
for the rest of the story.
The antiviral effect may be essentially unrecognizable, but the cumulative
destruction can lead to a serious condition known as cirrhosis. Cirrhosis
is caused by progressive destruction and regeneration of hepatocytes,
inflammation, and scarring.
This terribly compromises the function of the liver and shortens
the life of the patient if the disease is severe, and it can progress
to cancer, says Chisari.
The scar tissue impedes blood flow in the liver. The decreased blood
flow can then cause a number of other complications to the body, including
jaundice, which can be seen as a yellow coloring of the eyes and skin
because of the release of bile into the bloodstream. Cirrhosis itself
often kills chronically infected patients, and even when it does not it
can lead to cancer of the liver.
Cancer is caused by the exposure of the liver to mutagens released by
the inflammatory cells and to an increased probability of random point
mutations due to the active regeneration spurred on by the continual CTL
"[People with chronic hepatitis] have a 100- to 200-fold increased
risk for developing liver cancer," says Chisari. "By comparison,
heavy smokers have a 10-fold higher risk of developing lung cancer."
In all, 15 to 25 percent of people who are chronically infected with
HBV die from liver disease. In the United States, liver diseases related
to HBV infections claim about 5,000 lives a year. Worldwide, this number
is 1 million per year.
The situation is particularly dire for children. Nine out of ten infants
who are infected with HBV will suffer a chronic infection, whereas only
two to five percent of individuals who are infected as adults will become
chronically infected. In fact, the CDC estimates that 20 to 30 percent
of the 1.25 million Americans who are chronically infected with HBV were
infected as children.
A Less Vigorous Defense
HBV infections are more serious in chronically infected patients because
their immune systems mount a quantitatively inadequate defense. Thats
why infants are at a dramatically increased risk of acquiring a chronic
infection if they are infected by their mothers through neonatal transmission
when their immune systems are immature. The virus establishes itself in
this immunologically immature population and tolerizes them so that they
will not make an adequate immune response.
When the viral infection spreads, so does the amount of viral antigen
in the blood. The immune system recognizes specific antigens, or epitopes
and uses this recognition as the basis of a targeted attack. Chisaris
group first discovered in the late 1980s that people who clear the infection
make a polyclonal, vigorous response to many different epitopes from all
the viral proteins.
"Its a profound and effective immune response directed at
so many elements that mutational escape [is not possible]," says
In chronically infected patients, on the other hand, the response is
rather weak. Several years ago, Chisari looked at the immune response
in infected humans by comparing virus-specific cytotoxic T cells with
characteristics of the disease. When he looked at the blood of chronically
infected patients, Chisari saw few cytotoxic T lymphocytes and the ones
that were there were specific for very few epitopes. This profound difference,
suggests Chisari, is the basis for chronic infection.
"Chronically infected patients develop an ineffective immune response,"
he says. "If we can find some way to boost this immune response that
they are, in fact, capable of making but are not, maybe they would then
Current treatment for chronic HBV involves taking antivirals, which
control but do not eliminate the infection. As soon as the course of medicine
is stopped, the HBV rebounds. Chisari and his collaborators are now looking
for ways to couple antiviral therapy with immune stimulation.
The General Clinical Research Center
Significantly, Chisari carries out a number of his studies at the General
Clinical Research Center (GCRC), which he also directs.
"If there is one thing you can do in this article," Chisari
says to me, "bring the GCRC to the attention of the TSRI faculty
and postdoctoral fellows."
The GCRC is a TSRI-managed clinical research facility located in the
Green Hospital. The center is open to any TSRI-affiliated investigator
or postdoctoral fellow who is interested in clinical studies involving
humans, and it provides substantial financial assistance for these studies
by providing for the care, monitoring, and testing of patients.
"[Investigators] dont need to seek additional funding to
pay for the patient-related costs," says Chisari.
In fact, the GCRC enables TSRI investigators to determine definitively
the bearing of their discoveries on human biology. It brings together
basic scientists with physicians and nurses who are trained to take care
of patients and collect valuable samples. The center has a laboratory,
directed by TSRI Associate Professor Daniel Salomon, that processes samples
to stabilize them for further study. The center also has a large database
to track samples and draws upon the talents of TSRI Professor James Koziol,
"It has been used very effectively by a number of TSRI investigators
and also by a large number of clinical investigators," says Chisari,
who is the GCRC director. Associate Professor Bruce Zuraw is associate
director. Professor Ernest Beutler, Chair of the Department of Molecular
and Experimental Medicine, is the principal investigator on the grant
from the National Institutes of Health, which provides the majority of
the GCRCs funding and provides strict guidelines designed to protect
the rights and safety of patients in any human trial.
Any researcher who wishes to conduct a study in the GCRC must submit
a protocol to the TSRI Human Subjects Committee, which is independent
of the GCRC. This committee reviews the safety, ethical, and human-protection
aspects of the study. If the protocol passes, it is then reviewed by the
GCRC Scientific Advisory Committee, which meets every month or so to evaluate
proposed studies for scientific merit.
Chisari notes that this procedure is supportive of scientists while
rigorously enforcing National Institutes of Health guidelines. Investigators
who are using the GCRC will be alerted to any risks and provided with
education and guidance on how they can be avoided, he says.
TSRI researchers who are interested in using the facilities establish
a collaboration with a clinician who has admitting privileges to the hospital,
and the studies are carried out by this licensed physician.
Investigators use the GCRC for a number of purposes, the simplest of
all being to safely obtain blood for their investigations. The center
tracks blood donors and screens all blood for HIV and hepatitis B and
A slightly more involved study might find a TSRI investigator correlating
some marker in blood or other bodily fluid with the manifestation of a
disease. The investigator might, for instance, ask the doctors and nurses
at the GCRC to conduct clinical exams of a study group to monitor patients'
progress, at the same time as collecting samples. Clinical exams can range
from routine interviews and X-rays to magnetic resonance imaging and spinal
At the highest level, the GCRC provides a way to bring together patients
with diseases and conditions for which there is no known cure with investigators
who have potential therapies. And during such clinical investigations,
the center can monitor the procedures for beneficial or adverse effects,
drug levels in the blood, pharmacokinetics, and toxicology.
"It could be an important outlet for chemists who make small molecules
they think could be important in the life of a cell or the life of an
organism," says Chisari. "A treatment can be administered to
the patient in the setting of the GCRC once approval is obtained by [TSRIs
Institutional Review Board] and by the U.S. Food and Drug Administration."
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