Harvard’s David Altshuler on the Complex
Genetics of Diabetes
As decades go, the last was the scientific equivalent of a gold rush: "One
of the most prolific periods of discovery in human genetics," as a New
England Journal of Medicine essay recently described it (J.N.
Hirschhorn, 360: 1699-1701, 2009). First the human genome sequence was
published in 2003, followed five years later by a catalog, known as HapMap,
of common genetic variation across that genome. By then, genome-wide
association studies had begun documenting the association of common genetic
variations with chronic conditions such as heart disease and
diabetes. By the end
of last year, geneticists had already identified more than 250 gene
variants associated with over 40 different chronic diseases and human
"...surprisingly enough, we don’t really have
good methods yet to take a gene of unknown function and
figure out what it’s doing."
At the forefront of this tidal wave of research is the Harvard geneticist
and endocrinologist David Altshuler, whose 13 Hot Papers tracked during the
course of 2009 placed him near the top of this publication’s annual
ranking of the year’s hottest scientists (Science Watch,
March/April 2010). Altshuler is a co-author on half a dozen papers that
have received over 1,000 citations each in the past decade, and he’s
the first author on the 2005 Nature article—"A haplotype map
of the human genome"—that has garnered more than 2,000 citations in
less than five years (see table below). Another 20 of
Altshuler’s articles have garnered over 100 citations each.
Altshuler, 45, earned his Bachelor’s of Science from the
Massachusetts Institute of Technology in 1986 and then obtained an M.D. and
his Ph.D. at Harvard in 1994. After doing his internship and residency at
Massachusetts General Hospital, he began a clinical fellowship there in
endocrinology in 1996, coincident with a postdoctoral fellowship in
also) at MIT’s Whitehead Institute. In 2000, Altshuler started
his own laboratory at Massachusetts General Hospital and Harvard Medical
School, where he’s now a professor of genetics and medicine.
Altshuler is also a founding member and deputy director of the Broad
Institute of MIT and Harvard.
Altshuler spoke to Science Watch from his
home in Brookline, Massachusetts.
Considering the enormous progress made in the last
decade in human genetics, there’s been considerable controversy
about whether we’ll ever learn enough to predict our risk of
disease from our genotypes. Does this bother you?
In my mind, the primary goal is not to predict disease, nor to personalize
medicine. It’s to understand the biological systems that underlie
common diseases—type 2 diabetes, for example, which is my research
focus. The problem that got me started is very simple: why is it that some
people living in our modern society and environment gain weight and others
not? Why do some people who become
also get diabetes, and others not?
If we could figure this out, we’d understand the biological basis of
diabetes—and if we knew the basis we could rationally design
approaches to prevention and therapy.
How do we figure out the basis of a disease? One approach is to study it in
cells, and in mice—to hypothesize that diabetes is a disorder of
insulin resistance, or of fat cells, or muscle. This approach can clearly
identify fundamental biological mechanisms, but it can’t tell us
which mechanisms actually apply in patients. And it might, in fact, lead us
"I never imagined that a disease like diabetes was going to
turn out to be explained by only five or ten genes," says
David Altshuler of Harvard Medical School and the Broad
Photo by Len Rubenstein
So, another approach is based on the observation that the diseases run in
families, and not to prejudge whether it’s insulin resistance, or
whether it’s the fat cell or the muscle cell. Instead, we can simply
follow the disease in families and in the population, and track down the
genes that influence risk. And if we can find those genes—and
we’re just beginning with this, we’re still in the early
days—and if we can figure out what those genes do biologically, that
can tell us about the underlying root cause of the disease in human
So what kind of progress have we made on
In the 1990s, six genes were found that contribute powerfully to risk in
rare families with a so-called "Mendelian" form of type 2 diabetes. And by
2003 it was clear that a couple of biological "candidate genes" also played
a role. In sum, however, these genes explained less than 1% of the risk of
type 2 diabetes.
In the last five, years, using so-called genome-wide association studies,
we’ve now identified the genomic locations, at least, of three dozen
genes that influence risk of diabetes. I use the word "locations"
intentionally; we haven’t yet precisely defined the specific genes
and mutations responsible in each case.
Using the methods to date, all we can say is that each variant identifies a
place in the human genome where genetic variants track with disease. That
tells us there must be a gene in that region that is somehow affecting
susceptibility to the disease.
What we have to do now as a field, among many other things, is nail down
exactly which gene is responsible in each case—or could it be two or
three genes?—and exactly what they do biologically. What tissues do
they operate in? If we can figure this out, it will tell us a lot of new
information about the underlying biology of the disease in humans.
Using diabetes as our example again, have we
learned anything substantive yet about the underlying biology?
Well, it depends on how you define "substantive." At some level I’d
rather stress how much we have yet to learn, because our knowledge is still
so incomplete. The fact is, as I’ve mentioned, it’s early days
in the elucidation of the genetic basis of common diseases. We can,
however, point to some lessons.
One thing that I find very interesting, although it is somewhat
controversial, has to do with the proportion of diabetes genes that were
previously identified by other approaches. In 2005 we made a list of all
the genes that anyone had suggested might play a role in type 2 diabetes.
We did this by searching papers, and abstracts from diabetes-research
meetings. We came up with some 600 candidate genes that were already known
to play some role in glucose metabolism, or in animal or cellular models of
We then did our genome-wide association studies. We examined thousands of
patients who have diabetes, and thousands without diabetes. We compared
their genomes to find places that systematically differ in relation to
disease risk. And we found a couple of dozen such reproducible influences
on diabetes in humans. When we asked which of the 600 genes mapped to those
locations, the answer was, almost none.
What does this mean? That we don’t
understand diabetes, or that the genome-wide association studies
Well, it led some people to say there’s something wrong with our
method—that it’s telling us the wrong answer.
And you obviously don’t think
To be entirely honest, I have more faith in genetics than I do in what
journals tell us about the basis of disease. What’s interesting is
that if you take other diseases, such as autoimmune disorders, and you do
the same experiment—well, you find 100 different places in the genome
that affect the risk of autoimmune disease. And, in that group of diseases,
the answers make sense: you find genes that play a role in the immune
If you do the same experiment with cholesterol levels, and make a list of
genes influencing cholesterol levels in humans, you find genes that make
sense based on previous biology. You don’t find all the known genes,
of course, because not all genes have genetic variations in them. And you
find lots of new genes, because there is a lot left to learn.
But, certainly, in autoimmune disease and cholesterol, there is a big
overlap between the list of prior "candidate" genes and human genetics. In
fact, when my colleagues took glucose levels as the phenotype, rather than
type 2 diabetes, they found 15 regions in the genome that affect
blood-glucose levels. Almost all of them were on our list of 600 genes.
So how are we supposed to interpret this
divergence in the overlap between biological candidate genes for human
genetics—yes, for glucose level and autoimmune disease and
cholesterol, no for diabetes?
As someone biased toward human genetics, I take this as a referendum on how
well the model systems and prior research found the genes relevant to
humans (at least, relevant based on inheritance). What turns out to be the
case is that if you make a list of the genes that researchers say are
involved in diabetes, you do find most of the genes identified so far that
affect fasting glucose levels in healthy people. But you don’t find
many of the genes that seem to actually affect risk of type 2 diabetes the
Well, that kind of makes sense if you think about it. Imagine that I looked
for the genes that affect the control of day-to-day body temperature, and I
examined mice that had altered body temperature. I’d find a lot of
genes that influence the homeostasis of body temperature. But that might or
might not tell me about why people get a fever when they have an infection.
Normal homeostasis and biology might not be the same thing as
pathophysiology—the process that actually leads to disease.
You’re saying it speaks to our
underlying assumptions about the disease?
Yes. It comes back to what people’s assumptions are. There’s
been an assumption on many people’s part that the biology of glucose
must be the same as the biology of diabetes. And much of it is, of course;
I’m not saying there’s no overlap between those two. But
there’s lot of ways you can think that getting diabetes may not be
the same as how you regulate blood sugar, day to day, or may not be
captured by studying the basic biology of cells in a dish.
Another criticism of this kind of work is
that the genes found so far explain only a very small percentage of the
genetic variation in diabetes. Is that disappointing?
Some people seem to think so, but I don’t. To be honest, I was much
more worried about failing completely than I was confident that we’d
explain everything! I never imagined that a disease like diabetes was going
to turn out to be explained by only five or ten genes.
Highly Cited Papers by David
and Colleagues, Published Since
(Ranked by citations)
S.B. Gabriel, et al.,
"The structure of haplotype
blocks in the human genome,"
Science, 296(5576): 2225-9,
Intl. HapMap Consortium (D. Altshuler,
et al.), "A haplotype
map of the human genome,"
Nature, 437(7063): 1299-1320,
Intl. SNP Map Working Group (R.
Sachidanandam, et al.),
"A map of human genome sequence
variation containing 1.42 million
Nature, 409(6822): 928-33,
M. Cargill, et al.,
single-nucleotide polymorphisms in
coding regions of human
Genetics, 22(3): 231-8, 1999.
V.K. Mootha, et al.,
"PGC-1 alpha-responsive genes
involved in oxidative phosphorylation
are coordinately downregulated in human
Genetics, 34(3): 267-73, 2003.
D. Altshuler, et al.,
"The common PPAR gamma Pro12Ala
polymorphism is associated with
decreased risk of type 2
Genetics, 26(1): 76-80, 2000.
R. Saxena, et al.,
analysis identifies loci for type 2
diabetes and triglyceride
316(5829): 1331-6, 2007.
E. Zeggini, et al.,
"Meta-analysis of genome-wide
association data and large-scale
replication identifies additional
susceptibility loci for type 2
Genetics, 40(5): 638-45, 2008. 317
Keep in mind that when we started doing these studies, about 1% of the
variability in type 2 diabetes was explicable by known genetic factors.
It’s gone up in three years to 10%. If you go back and read the
literature, you’ll be hard-pressed to find anyone who wrote that the
genetics of complex, common diseases was going to be due to only a few
common variants—and you’ll find others who argued that
genome-wide association studies weren’t going to work at all, that
nothing would be found. Certainly, that was a reasonable point of view, as
all previous efforts to understand the genetics of common disease had
In light of this, it’s clear that the hundreds of reproducible
variations that have been found for dozens of diseases are a striking
success. Having said this, it’s also clear that the road from initial
genetic mapping to understanding what we’ve learned—let alone
applying it to medicine—is long.
Moreover, it’s also clear that the ultimate answer is going to be
that diabetes is genetically very complicated—that there are many,
many processes that could probably contribute to diabetes. And, in each
such biological process, there are many genetic variations. Some of those
will be common. Some of them will be rare. Some will directly affect
diabetes risk, while some will affect obesity, say, and so only indirectly
This is very fundamental to where we are in human genetics. We’re
trying to put together a holistic picture of the human body that says,
look, things that are common and complex like diabetes are actually common
because there’s a lot of ways to get to them, and they are indeed
complex. And in the end there will be multiple processes, and there will be
many genetic variants and many environmental exposures, and each one of
them alone will explain only a very small percentage of that variation.
Some people say this is too complex, and that we should only study simple
cases where one gene is responsible, or mice we’ve engineered to have
only one mutation at play. Those things are very important, but I find it
hard to understand how we’ll ever know we’ve understood
diabetes if we turn our back on the evident complexity that exists in the
patient. Especially now that we have methods that actually work!
Ultimately, how far do you think
you’ll get with genome-wide association studies, and what will you
have learned when you get there?
First of all, it depends on what you mean by "genome-wide association
studies." That term has come to mean the first wave of studies that
compared the set of common variants we had catalogued by 2005. However,
when I think about it, I think of testing all the genetic variation that
exists in the patient. Most of our effort for the last couple of years has
been aimed at obtaining a more complete understanding—developing and
applying next-generation sequencing and other methods to query all the
genetic variation in each patient.
So, if you broaden the term genome-wide association study to mean testing
all the DNA variation in each patient for its relationship to disease, well
then, I think we’re still at least five years away from knowing how
far we can get with this approach. So, let’s say five years from now
we’ve sequenced the genomes of many, many diabetics, and not just of
diabetics but of many other phenotypes that are relevant—obesity and
high fasting glucose and so on—by then I think we’ll have
identified 100 or 200 genes that are affecting these traits in humans.
Well, that’s 1% of the genome—200 genes out of 20,000. It makes
sense to me that it will be some number like that. Not five genes. How
could it be? My colleague Gary Ruvkun published a paper in Nature
years ago showing that if you systematically knocked out each of the genes
in a worm, and studied the fat cells, then 500 genes influenced that
phenotype. If 500 genes influence fat biology in a worm, how many influence
diabetes in a human?
My guess is that if we knew those 200 genes and studied them, we’d
find they are involved in five or ten main processes. That is, each process
contains multiple genes, and there are many processes that contribute to
disease. But, if we know which processes they are, we can study them to
figure out how they lead to diabetes. I would see this as a big success.
I don’t measure the success by whether we’re up to 30% of the
heritability or 70%. And I certainly don’t measure the success based
on whether or not I can predict in the clinic what’s going to happen
to any particular patient. Because even if I take identical twins, I
can’t predict in the clinic what’s going to happen a lot of the
time. And, as a physician, I never found prediction to be rewarding unless
we had something to offer that really helped the patient. And those cures
don’t exist, and won’t exist unless we better understand the
root cause of the disease in our patients.
So, if we could understand the biology underlying diabetes, and if that was
in textbooks and the next generation could base their research and medical
practice on that foundation, well, that would seem to me like really a big
Another startling finding from these studies
is that many of the gene variants found so far are in non-coding regions
of the genome. How do you interpret that?
Some people certainly consider that a surprise, and many find it
disappointing. That’s because they’re used to thinking in terms
of Mendelian genetics, where if you have a very strong phenotype,
it’s often due to a coding mutation. And, certainly, most of biology
has focused on the coding regions of genes. So, scientists are comfortable
But if you think about it, you could have predicted that this would be the
case if you compare the human genome to the genome of the mouse and the cow
and the dog and the chimp, and you say, show me the parts of the genome
that are conserved throughout evolution. One thing you find is that all the
exons—the stretches of DNA that actually code for proteins—are
conserved. That’s been known for a long time, and that fits the
model: things that are functional are conserved across evolution.
But now turn it around and ask how much of the human genome is conserved
across species? The answer is about 6%. Exons make up about 1.5% of the
genome. In other words, three-quarters of the DNA in your genome that
matters, based on evolution, is non-coding. Now, that’s not what
matters to a textbook—that’s what matters to evolution. And
evolution works at the level of fitness and function. It says that most of
the functional DNA in our genome is non-coding, and if that’s right,
then most of the variation in nature that influences phenotype must also be
But because we as biologists don’t yet know how to interpret
non-coding DNA variations, there’s a lot of disappointment and
frustration that genome-wide association studies point to non-coding
sections. It’s not disappointing! It’s why we did it—to
learn things we didn’t already know. And it says we need to learn how
to interpret non-coding DNA, not because of genome-wide association
studies, but because evolution has told us that that’s where
three-quarters of the functional DNA in our genomes resides.
What are the big issues that still have to
be addressed in human genetics? What are the outstanding
Well, we’re moving toward a world in which so many species have had
their genomes sequenced, and many individuals in each species. And
certainly in humans, mice, and flies, there will be lots of correlations
between genotype variation and phenotype variation. So, once we’ve
sorted through the data and figured out which relationships are durable,
the big question is going to be, how do the changes in DNA affect function
at the level of molecular biology, of cells, of tissues, and of whole
organisms. That’s one obvious question.
Another question is, how do we take a gene of unknown function and figure
out what biology it’s involved in? We are going to be increasingly
able to say, well, here are the 100 genes that are involved in lupus, or
heart disease, or cancer, but most of them we know nothing about. No papers
exist to tell us about them. We don’t have cellular models or animal
models that tell us what’s going on.
And, surprisingly enough, we don’t really have good methods yet to
take a gene of unknown function and figure out what it’s doing. The
biggest problem today with genetic studies is not that they haven’t
explained enough of the heritability—it’s that when new genes
are found, it’s very hard to figure out what they do. And, as the
bottleneck of gene discovery is overcome, the next bottleneck looms large.
The third issue, of course, is that even if we knew all the genes that
influence risk of a disease, and what biology they’re involved
in—who cares, unless we can find some ways to use that information to
help a patient? The geneticist’s credo is that the patient leads you
to the genes and the genes lead you to the biology. But the real goal is to
develop an intervention that prevents or cures the disease.
I realize that in the last 13 years since I finished my medical training I
could have done more direct good for patients by staying in clinical
medicine than by doing this research. But I also believe that if in the end
we can discover important new insights about the causes of diabetes, at
some point the ledger with turn positive. I’m a big believer in the
long-term value of fundamental understanding, and I think genetics is one
of the best tools we have to figure out disease. I’m excited to spend
the next 20 years seeing how the story turns out!
KEYWORDS: David Altshuler, diabetes, type 2 diabetes, genome-wide
association studies, gene mapping, genome sequencing.