The completion of the Human Genome Project in 2004, along with the
sequencing of nonhuman genomes, has spawned an incredible revolution
in the understanding of genetics. Simultaneously, geneticists have raced to
develop medicines to treat and cure diseases caused by genes gone awry.
Gene therapy, treatment that gets at the direct cause of genetic disorders,
is sometimes touted as the magic bullet, the cure-all for inherited diseases
(see Chapter 13 for a partial list) and cancer (see Chapter 14). Gene therapy
may even provide a way to block the genes of pathogens such as the virus
that causes AIDS, providing reliable treatments for illnesses that currently
have none.
Unfortunately, the shining promise of gene therapy has been hampered by a
host of factors including finding the right way to supply the medicine to
patients without causing new or worse problems than the ones being treated.
In this chapter, you examine the progress and perils of gene therapy.
Monday, April 13, 2009
Curing Genetic Disease
Take a glance back through for proof that your health and
genetics are inextricably linked. Not only do mutations cause disorders that
are passed from generation to generation, but mutations acquired during
your lifetime can have unwanted consequences such as cancer. And your
own genes aren’t the only ones that cause complications — the genes carried
by bacteria, parasites, and viruses lend a hand in spreading disease and
dismay worldwide.
genetics are inextricably linked. Not only do mutations cause disorders that
are passed from generation to generation, but mutations acquired during
your lifetime can have unwanted consequences such as cancer. And your
own genes aren’t the only ones that cause complications — the genes carried
by bacteria, parasites, and viruses lend a hand in spreading disease and
dismay worldwide.
Curing Genetic Disease
Take a glance back through Part III of this book for proof that your health and
genetics are inextricably linked. Not only do mutations cause disorders that
are passed from generation to generation, but mutations acquired during
your lifetime can have unwanted consequences such as cancer. And your
own genes aren’t the only ones that cause complications — the genes carried
by bacteria, parasites, and viruses lend a hand in spreading disease and
dismay worldwide.
genetics are inextricably linked. Not only do mutations cause disorders that
are passed from generation to generation, but mutations acquired during
your lifetime can have unwanted consequences such as cancer. And your
own genes aren’t the only ones that cause complications — the genes carried
by bacteria, parasites, and viruses lend a hand in spreading disease and
dismay worldwide.
Finding Vehicles to Get Genes to Work
The first step in successful gene therapy is designing the right delivery system
to introduce a new gene or shut down an unwanted one. The delivery
system for gene therapy is called a vector. A perfect vector
Must be innocuous so that the recipient’s immune system doesn’t reject
or fight the vector.
Must be easy to manufacture in large quantities. Just one treatment may
require over 10 billion copies of the vector because you need one delivery
vehicle for each and every cell in the affected organ.
Must be targeted for a specific tissue. Gene expression is tissue-specific
(see Chapter 10 for details), so the vector has to be tissue-specific, too.
Must be capable of integrating its genetic payload into each cell of the
target organ so that new copies of each cell generated later on by mitosis
contain the gene therapy payload.
to introduce a new gene or shut down an unwanted one. The delivery
system for gene therapy is called a vector. A perfect vector
Must be innocuous so that the recipient’s immune system doesn’t reject
or fight the vector.
Must be easy to manufacture in large quantities. Just one treatment may
require over 10 billion copies of the vector because you need one delivery
vehicle for each and every cell in the affected organ.
Must be targeted for a specific tissue. Gene expression is tissue-specific
(see Chapter 10 for details), so the vector has to be tissue-specific, too.
Must be capable of integrating its genetic payload into each cell of the
target organ so that new copies of each cell generated later on by mitosis
contain the gene therapy payload.
viruses are the favored vector
Currently, viruses are the favored vector. Most gene therapies aim to put a
new gene into the patient’s genome, so it’s pretty easy to understand why
viruses are appealing candidates for vectorhood — this gene-sharing action
is almost precisely what viruses do naturally.
new gene into the patient’s genome, so it’s pretty easy to understand why
viruses are appealing candidates for vectorhood — this gene-sharing action
is almost precisely what viruses do naturally.
virus latches onto a cell
When a virus latches onto a cell that isn’t somehow protected from the virus,
the virus hijacks all that cell’s activities for the sole purpose of making more
viruses. Viruses reproduce this way because they aren’t really alive and have
no moving parts of their own to accomplish reproduction. Part of the virus’s
attack strategy involves integrating virus DNA into the host genome in order
to execute viral gene expression. The problem is that when a virus is good at
attacking a cell, it causes an infection that the patient’s immune system
fights. So the trick to using a virus as a vector is taming it.
the virus hijacks all that cell’s activities for the sole purpose of making more
viruses. Viruses reproduce this way because they aren’t really alive and have
no moving parts of their own to accomplish reproduction. Part of the virus’s
attack strategy involves integrating virus DNA into the host genome in order
to execute viral gene expression. The problem is that when a virus is good at
attacking a cell, it causes an infection that the patient’s immune system
fights. So the trick to using a virus as a vector is taming it.
Gentling a virus for use as a vector
Gentling a virus for use as a vector usually involves deleting most of its genes.
These deletions effectively rob the virus of almost all its own DNA, leaving only
a few bits. These remaining pieces are primarily the parts normally used by the
virus for getting its DNA into the host.
These deletions effectively rob the virus of almost all its own DNA, leaving only
a few bits. These remaining pieces are primarily the parts normally used by the
virus for getting its DNA into the host.
“Inserting Healthy Genes into the Picture
“Inserting Healthy Genes into the Picture” section of this
chapter, the scientist splices a healthy gene sequence into the virus to replace
the deleted parts of the viral genome. Like the delivery truck drivers that bring
packages to your doorstep, a helper is needed to move the payload from the
virus to the recipient cell. The scientist sets up another virus particle with
some of the deleted genes from the vector. This second virus, called a helper,
makes sure that the vector DNA replicates properly.
chapter, the scientist splices a healthy gene sequence into the virus to replace
the deleted parts of the viral genome. Like the delivery truck drivers that bring
packages to your doorstep, a helper is needed to move the payload from the
virus to the recipient cell. The scientist sets up another virus particle with
some of the deleted genes from the vector. This second virus, called a helper,
makes sure that the vector DNA replicates properly.
Geneticists conducting gene therapy
Geneticists conducting gene therapy have several viruses to choose from as
possible delivery vehicles (vectors). These viruses fall into one of two classes:
Those that integrate their DNA directly into the host’s genome
Those that climb into the cell nucleus to become permanent but separate
residents (called episomes)
Within these two categories, three types of viruses — oncoretroviruses,
lentiviruses, and adenoviruses — are popular choices for gene therapy.
possible delivery vehicles (vectors). These viruses fall into one of two classes:
Those that integrate their DNA directly into the host’s genome
Those that climb into the cell nucleus to become permanent but separate
residents (called episomes)
Within these two categories, three types of viruses — oncoretroviruses,
lentiviruses, and adenoviruses — are popular choices for gene therapy.
Viruses
Viruses that join right in
Two popular viruses for gene therapy integrate their DNA directly into the
host’s genome. Oncoretroviruses and lentiviruses are retroviruses that transfer
their genes into the host genome; when the retrovirus genes are in place,
they’re replicated right along with all the other host DNA. Retroviruses use
RNA instead of DNA to code their genes; these viruses use a process called
reverse transcription (described in Chapter 10) to convert their RNA into
DNA, which is then inserted into a host cell’s genome.
Two popular viruses for gene therapy integrate their DNA directly into the
host’s genome. Oncoretroviruses and lentiviruses are retroviruses that transfer
their genes into the host genome; when the retrovirus genes are in place,
they’re replicated right along with all the other host DNA. Retroviruses use
RNA instead of DNA to code their genes; these viruses use a process called
reverse transcription (described in Chapter 10) to convert their RNA into
DNA, which is then inserted into a host cell’s genome.
Oncoretroviruses
Oncoretroviruses, the first vectors developed for gene therapy, get their name
from oncogenes, which turn the cell cycle permanently on — one of the precursors
to development of full-blown cancer. Most of the oncoretrovirus vectors in
use for gene therapy trace their history back to a virus that causes leukemia in
monkeys (it’s called Moloney murine leukemia virus, or MLV). MLV has proven
an effective vector, but it’s not without problems; MLV’s propensity to cause
cancer has been difficult to keep in check. Oncoretroviruses work well as vectors
only if they’re used to treat cells that are actively dividing.
from oncogenes, which turn the cell cycle permanently on — one of the precursors
to development of full-blown cancer. Most of the oncoretrovirus vectors in
use for gene therapy trace their history back to a virus that causes leukemia in
monkeys (it’s called Moloney murine leukemia virus, or MLV). MLV has proven
an effective vector, but it’s not without problems; MLV’s propensity to cause
cancer has been difficult to keep in check. Oncoretroviruses work well as vectors
only if they’re used to treat cells that are actively dividing.
Lentiviruses
Lentiviruses, on the other hand, can be used to treat cells that aren’t dividing.
You’re probably already familiar with a famous lentivirus: HIV. Vectors for
gene therapy were developed directly from the HIV virus itself. Although the
gutted virus vectors contain only 5 percent of their original DNA, rendering
them harmless, lentiviruses have the potential to regain the deleted genes if
they come in contact with untamed HIV virus particles (that is, the ones that
infect people with AIDS). Lentiviruses are also a bit dicey because they tend
to put genes right in the middle of host genes, leading to loss-of-function
mutations
You’re probably already familiar with a famous lentivirus: HIV. Vectors for
gene therapy were developed directly from the HIV virus itself. Although the
gutted virus vectors contain only 5 percent of their original DNA, rendering
them harmless, lentiviruses have the potential to regain the deleted genes if
they come in contact with untamed HIV virus particles (that is, the ones that
infect people with AIDS). Lentiviruses are also a bit dicey because they tend
to put genes right in the middle of host genes, leading to loss-of-function
mutations
HIV lentivirus vectors
HIV lentivirus vectors are used to combat AIDS. The vector virus carries a
genetic message that gets stored in the patient’s immune cells. When HIV
attacks these immune cells, the vector DNA blocks the attacking virus from
replicating itself, effectively protecting the patient from further infection. So
far, this treatment seems to work and substantially reduces the amount of
virus carried by affected persons.
genetic message that gets stored in the patient’s immune cells. When HIV
attacks these immune cells, the vector DNA blocks the attacking virus from
replicating itself, effectively protecting the patient from further infection. So
far, this treatment seems to work and substantially reduces the amount of
virus carried by affected persons.
Viruses that are a little standoffish
Adenoviruses are excellent vectors because they pop their genes into cells
regardless of whether cell division is occurring. Adenoviruses have been both
promising and problematic. On the one hand, these viruses are really good at
getting into host cells. On the other hand, adenoviruses tend to excite a strong
immune response — the patient’s body senses the virus as a foreign particle
and fights it. To combat the immune reaction, researchers have worked to
delete the genes that make adenoviruses easy for the host to recognize.
regardless of whether cell division is occurring. Adenoviruses have been both
promising and problematic. On the one hand, these viruses are really good at
getting into host cells. On the other hand, adenoviruses tend to excite a strong
immune response — the patient’s body senses the virus as a foreign particle
and fights it. To combat the immune reaction, researchers have worked to
delete the genes that make adenoviruses easy for the host to recognize.
Adenoviruses
Adenoviruses don’t put their DNA directly into the host genome. Instead,
they exist separately as episomes, so they aren’t as likely to cause mutations
as lentiviruses. The drawback is that the episomes aren’t always replicated
and passed on to daughter cells when the host cell divides. Nonetheless,
adenovirus vectors have been used with notable success — and failure. (See
“Making Slow Progress on the Gene Therapy Front” at the end of the chapter
for the details.)
they exist separately as episomes, so they aren’t as likely to cause mutations
as lentiviruses. The drawback is that the episomes aren’t always replicated
and passed on to daughter cells when the host cell divides. Nonetheless,
adenovirus vectors have been used with notable success — and failure. (See
“Making Slow Progress on the Gene Therapy Front” at the end of the chapter
for the details.)
Inserting Healthy Genes into the Picture
Finding the right delivery system is a necessary step in mastering gene therapy,
but to nab genes and put them to work as therapists, geneticists must
also find the right ones. Because finding healthy genes isn’t simple, gene
mapping is still a major obstacle in the road to implementing gene therapy.
Imagine you’re handed a man’s photograph and told to find him in New York
City — no name, no address, no phone number. The task of finding that man
includes figuring out his identity (maybe by finding out who his friends are),
figuring out what he does for a living, narrowing your search to the borough
he lives in, and identifying his street, block, and, finally, his address. This
wild-goose chase is almost exactly like the gargantuan task of finding genes.
but to nab genes and put them to work as therapists, geneticists must
also find the right ones. Because finding healthy genes isn’t simple, gene
mapping is still a major obstacle in the road to implementing gene therapy.
Imagine you’re handed a man’s photograph and told to find him in New York
City — no name, no address, no phone number. The task of finding that man
includes figuring out his identity (maybe by finding out who his friends are),
figuring out what he does for a living, narrowing your search to the borough
he lives in, and identifying his street, block, and, finally, his address. This
wild-goose chase is almost exactly like the gargantuan task of finding genes.
tool geneticists
Until recently,
the only tool geneticists had in the search for genes was the observation of
patterns of inheritance (like those shown in Chapter 12) and the subsequent
comparisons of how various groups of traits were inherited. This method,
called linkage analysis, is used to construct gene maps (see Chapter 4).
With the advent of DNA sequencing (see Chapter 11), however, the search
for names and addresses of genes has reached a whole new level (but the
search still isn’t over; see the sidebar “The role of the Human Genome
Project”).
the only tool geneticists had in the search for genes was the observation of
patterns of inheritance (like those shown in Chapter 12) and the subsequent
comparisons of how various groups of traits were inherited. This method,
called linkage analysis, is used to construct gene maps (see Chapter 4).
With the advent of DNA sequencing (see Chapter 11), however, the search
for names and addresses of genes has reached a whole new level (but the
search still isn’t over; see the sidebar “The role of the Human Genome
Project”).
geneticists hook up with a giant network of people to nail down the exact locations of genes:
1. Physicians identify a disorder by observing a phenotype caused by
mutation. Essentially, this is the face of the gene.
2. Genetic counselors work with patients and their families to gather complete
medical histories (see Chapter 12). Analysis of family trees may
uncover other traits that associate with the disorder.
3. Cell biologists look at the karyotypes of many affected people and link
traits to obvious chromosomal abnormalities. These large-scale changes
in chromosomes often provide hints about where genes reside. (Chapter
15 examines methods of karyotyping.)
4. Population geneticists analyze the DNA of large groups of people with
and without the disease to narrow down which chromosomes and which
genes are involved with the disease.
5. Biochemists study the chemical processes in the affected organs of
people with the disease to identify the physiology of the disorder. Often,
they’re able to nab the precise protein-gone-wrong.
6. With the protein in hand, geneticists use the genetic code (profiled in
Chapter 9) to work backwards from the building blocks of that protein,
the specific amino acids, to discern what the mRNA instructions were.
mutation. Essentially, this is the face of the gene.
2. Genetic counselors work with patients and their families to gather complete
medical histories (see Chapter 12). Analysis of family trees may
uncover other traits that associate with the disorder.
3. Cell biologists look at the karyotypes of many affected people and link
traits to obvious chromosomal abnormalities. These large-scale changes
in chromosomes often provide hints about where genes reside. (Chapter
15 examines methods of karyotyping.)
4. Population geneticists analyze the DNA of large groups of people with
and without the disease to narrow down which chromosomes and which
genes are involved with the disease.
5. Biochemists study the chemical processes in the affected organs of
people with the disease to identify the physiology of the disorder. Often,
they’re able to nab the precise protein-gone-wrong.
6. With the protein in hand, geneticists use the genetic code (profiled in
Chapter 9) to work backwards from the building blocks of that protein,
the specific amino acids, to discern what the mRNA instructions were.
right protein and backtracking to the mRNA
Identifying the right protein and backtracking to the mRNA pattern is extremely
helpful, but it still doesn’t divulge the identity of the gene. (Problems include
the fact that mRNAs are often heavily edited before they’re translated into
proteins [see Chapter 9] and the fact that the code is degenerate, meaning
that more than one codon can be used to get a particular amino acid). The
protein provides a general idea of what the gene address is, but it’s not precise
enough. To close in on the right address, the gene hunter has to sort through
the DNA itself.
helpful, but it still doesn’t divulge the identity of the gene. (Problems include
the fact that mRNAs are often heavily edited before they’re translated into
proteins [see Chapter 9] and the fact that the code is degenerate, meaning
that more than one codon can be used to get a particular amino acid). The
protein provides a general idea of what the gene address is, but it’s not precise
enough. To close in on the right address, the gene hunter has to sort through
the DNA itself.
gene-hunting
The entire gene-hunting safari depends on vast computer databases that are
easily accessed by the entire scientific community. These databases allow
investigators to search professional journals to keep up with new discoveries
by other scientists. Researchers are also constantly adding new pieces of the
puzzle, such as newly identified proteins, to storehouses of data.
easily accessed by the entire scientific community. These databases allow
investigators to search professional journals to keep up with new discoveries
by other scientists. Researchers are also constantly adding new pieces of the
puzzle, such as newly identified proteins, to storehouses of data.
Recombinant DNA technology
Recombinant DNA technology is the catchall phrase that covers most of the
methods geneticists use to examine DNA in the lab. The word recombinant is
used because DNA from the organism being studied is often popped into a
virus or bacteria (that is, it’s recombined with DNA from a different source)
to allow further study. Recombinant DNA is also used for a vast number of
other applications, including creating genetically engineered organisms
methods geneticists use to examine DNA in the lab. The word recombinant is
used because DNA from the organism being studied is often popped into a
virus or bacteria (that is, it’s recombined with DNA from a different source)
to allow further study. Recombinant DNA is also used for a vast number of
other applications, including creating genetically engineered organisms
n the case of gene therapy, recombinant DNA is used to
Locate the gene (or genes) that’s involved in a particular disorder or
disease.
Cut the desired gene out of the surrounding DNA.
Pop the gene into a vector (delivery vehicle) for transfer into the cells
where treatment is needed.
disease.
Cut the desired gene out of the surrounding DNA.
Pop the gene into a vector (delivery vehicle) for transfer into the cells
where treatment is needed.
The role of the Human Genome Project
Can’t geneticists just look up the genes they
need from all the sequencing data collected by
the Human Genome Project, or HGP? Someday
the answer will be yes, but we’re not there yet.
By 2005, 99 percent of the gene-rich part of the
genome (called the euchromatin) is fully
sequenced. That’s the good news. The bad
news for gene hunters is that a whopping 20
percent of the noncoding regions of the genome
still aren’t sequenced.
need from all the sequencing data collected by
the Human Genome Project, or HGP? Someday
the answer will be yes, but we’re not there yet.
By 2005, 99 percent of the gene-rich part of the
genome (called the euchromatin) is fully
sequenced. That’s the good news. The bad
news for gene hunters is that a whopping 20
percent of the noncoding regions of the genome
still aren’t sequenced.
The noncoding part of the genome
The noncoding part of the genome that’s mostly
junk DNA (the heterochromatin) has been tough
to work with because it’s made up of repetitive
sequences. All that repetition makes putting the
sequences into their proper order extremely difficult.
Some scientists think it may be another five
years before the Human Genome Project is truly
complete in the sense that the entire sequence
of the whole human genome is known. Even a
complete HGP leaves much left to learn;
junk DNA (the heterochromatin) has been tough
to work with because it’s made up of repetitive
sequences. All that repetition makes putting the
sequences into their proper order extremely difficult.
Some scientists think it may be another five
years before the Human Genome Project is truly
complete in the sense that the entire sequence
of the whole human genome is known. Even a
complete HGP leaves much left to learn;
HGP of the entire humane genome
Unfortunately, the maps constructed by the HGP
of the entire humane genome are drawn at the
wrong scale to be useful for pinpointing the
locations of genes. To get an idea of how scale
can be a problem, think about looking at a road
map. A low-resolution highway map can help
you find your way from one city to another, but
it can’t guide you to a very specific street
address in a particular city.
of the entire humane genome are drawn at the
wrong scale to be useful for pinpointing the
locations of genes. To get an idea of how scale
can be a problem, think about looking at a road
map. A low-resolution highway map can help
you find your way from one city to another, but
it can’t guide you to a very specific street
address in a particular city.
geneticists
What it comes down to is that geneticists have
only just started to explore the billions of base
pairs that contain the genetic instructions that
make humans tick. That’s why the gene hunt is
likely to go on for a long time to come.
only just started to explore the billions of base
pairs that contain the genetic instructions that
make humans tick. That’s why the gene hunt is
likely to go on for a long time to come.
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