Fall 2007 PDF - Whitehead Institute for Biomedical Research

Transcription

LIFE SCIENCES AT WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH
paradigm
Break
no eggs
PAGE 16
Behind the scenes of an
astonishing leap in
embryonic stem cell science
Q
AUTUMN 2007
eric s. brown is a technology
and science writer in the Boston area and a regular contributor to MIT Technology Insider.
sam ogden has been photographing for Whitehead,
among other clients, for about
20 years. His strength is in
translating complicated technologies into
dynamic and coherent images that are
understandable to all of us.
john soares has been capturing the essence of real people
in their real environments for
the past 16 years. He says his
work is either a modern twist on the classic
photographic aesthetic, or a classic twist on
the modern aesthetic.
peaco todd is a syndicated
cartoonist, the author and illustrator of several books, a professor at Vermont College and
Lesley University, and the creator of Porkbarrel Comix (www.porkbarrelcomix.com).
editor
Eric Bender
bender@wi.mit.edu
617.258.9183
associate editors
David Cameron
Alyssa Kneller
design
Eric Mongeon
Mongeon: Projects, Inc.
Office of
Communications
and Public Affairs
Whitehead Institute
for Biomedical
Research
5 Cambridge Center
Cambridge, MA
02142-1479
617.258.5183
www.whitehead.mit.edu
Paradigm is published twice a year by the
Office of Communications and Public Affairs at
Whitehead Institute for Biomedical Research.
The magazine reports on life sciences research
and innovations at Whitehead, and explores
public issues related to the conduct of biological
research. To subscribe, send your address to
publications@wi.mit.edu. Text, photographs and
artwork may not be reused without written permission from the editor.
window on whitehead
Freakonomics
and freakobiology
Surprise!
That’s the promise of Freakonomics, which appeared on the
bestsellers list in 2005 and can
still be found there. The book’s
subtitle is “A Rogue Economist Explores the Hidden Side of
Everything.” Aside from “everything,” it delivers on its promise.
The book covers the work of
Steven Levitt, who takes a clearheaded look at what actually
correlates among certain demographic and economic data. For
instance, he and his colleagues
find that Head Start participation doesn’t seem to affect school
performance, baby names trickle
down from higher- to lowerincome families, and gang members live with their mothers
because most of them are making
almost nothing.
You can also find other such
books by economic theorists on
bestseller lists, all with their own
neatly packaged surprises. One
of the best is The Black Swan,
which explores “The Impact of
the Highly Improbable” on decision-making. The title example
is from biology: European biologists confidently predicted that
all swans must be white … until
Australia was explored.
But you don’t see bestseller
books about basic biomedical research, although we’re awash in
its surprises. Why is that?
Clearly everyone expects surprises in biology. That’s one aspect that’s constant, whether
you’re a toddler at a zoo, an
elementary school child gazing through a microscope at an
amoeba, a high schooler joking
over praying mantises and their
distressing sex-with-a-snack practices, or an adult marveling at the
epic journeys of the tundra swan.
But molecular biology and its
closest buddies in the life sciences
can be a hard sell for the public.
One issue is that the molecular scale of the research is hard to
grasp. We’re talking about molecules that might be about 100millionth the size of a swan.
Another is the sheer complexity of the processes under
study. How dramatic is it to find
one more player in a molecular
pathway that already has more
players than the New England
Patriots—even if that pathway
makes you prone to a certain genetic disease or the proud possessor of beautiful brown eyes?
Well, there’s a shortcut to
seeing what’s really surprising:
watch for the advances that take
aback the scientists themselves.
There’s a big one in this issue’s
cover story.
Last year, Shinya Yamanaka of Kyoto University reported
stunning work in creating embryonic stem cell-like cells from
the cells of adult mice. “This is
at least as startling as Dolly,” the
cloned sheep, comments Whitehead Member Rudolf Jaenisch.
This year, Jaenisch’s lab was
among three that confirmed and
advanced those findings. By activating a mere four genes, you can
turn a mouse skin cell back into a
state that seems indistinguishable
from an embryonic stem cell.
Who knew?
As always, it’s anyone’s guess
as to which biomedical discoveries may trickle down to the clinic
and when. But for all of us, scientists and especially nonscientists,
the surprises are just beginning.
We may see some results in clinics, and maybe even bookstores,
sooner than we expect.
– Eric Bender
BROWN: STELLA JOHNSON
autumn 2007
among our contributors
contents
cover story
16
Break no eggs
Behind the scenes of an
astonishing leap in embryonic
stem cell science
features
7
Pumping up
Researchers probe the
diverse roles of mTOR
proteins in growth, cancer and
bodybuilding
10
Shedding light on
cancer stem cells
Cells created from scratch
to trigger breast cancer will
bring new evidence to a fierce
scientific debate
14
7
Pumping up
10
Shedding
light on cancer
stem cells
The human side of monkeypox
In the Congo, Kate Rubins and
colleagues study the smallpoxlike disease
22 State of research
If Massachusetts puts big bucks
into biomedical research, where
should the money go?
16
Break no eggs
24 Unsung heroines
While young researchers come
and go, career technicians keep
the labs humming
departments
2
Science digest
Cancer cells that enlist adult
stem cells, images from a deepultraviolet microscope, and
picky white blood cells
6
FastFAQs
What do university students
need to know about biology?
on the cover:
The mouse above offers
proof that researchers can
create embryonic stem
cells without using an egg.
It grew from an embryo
containing cells that had
been reprogrammed to an
embryonic state.
28 Whitehead tales
A colorful look at prion proteins
24
Unsung
heroines
PARADIGM : AUTUMN 2007
1
science digest
Antoine Karnoub has shown that mesenchymal stem cells can help cancer spread.
berg, who is also an MIT professor of
biology. “Rather, they might be influenced by the signals the cancer cell
experiences from stromal cells in the
context of the primary tumor.”
The conscripts that confer these
metastatic powers are mesenchymal
stem cells (MSCs), which generate
bone, muscle, cartilage and fat.
MSCs also play a critical role in
healing wounds. “Sites of tumor for-
“This study provides the
first evidence that a cancer
cell’s metastatic powers are
not necessarily intrinsic to the
cell itself.” - ROBERT WEINBERG
E
veryone knows that tumors are
packed with cancer cells, but
many normal cells live among
these deviants. The normal cells form
a structural framework called the
stroma, which was once thought to
resemble passive scaffolding. But a
growing body of research suggests
that cancer cells actively recruit normal cells from local and distant sites
to the scaffolding, where they release
signals that help the tumor thrive.
Beginning in 1999, several labs
increased primary tumor growth by
mixing cancer cells with fibroblasts
(cells that contribute to the formation
of connective tissue and the stroma of
tumors). This was the first proof that
stromal fibroblasts actively foster the
2
growth of cancer cells.
Working with a different type
of normal stromal cell, Whitehead
Member Robert Weinberg’s lab has
managed to facilitate metastasis—the
spread of cancer cells from the primary tumor to distant sites. Postdoctoral researcher Antoine Karnoub has
compelling evidence that some breast
cancer cells recruit normal adult stem
cells from the bone marrow and force
them to secrete a protein that fosters
cancer cell movement and invasion.
His results appeared online in Nature
in October.
“This study provides the first
direct evidence that a cancer cell’s
metastatic powers are not necessarily
intrinsic to the cell itself,” says Wein-
Plotting an invasion route
How did these lines of cancer cells
acquire the dangerous ability to
invade distant tissues?
Karnoub next examined the proteins made by the cells. He discovered
that MSCs ramp up their production
of the CCL5 protein in the presence of
JOHN SOARES
Cancer cells enlist adult stem cells
to promote metastasis
mation are much like open wounds,”
Karnoub says. “MSCs might very
well home to those sites to aid with
the healing process. Once there, they
may get entangled with the tumor
cells and actually help them grow.”
To investigate this idea, he combined MSCs from a human hip with
human breast cancer cells, implanted
the mixture into the backs of mice
and studied the growth of the resulting “mixed” tumors. As a control, he
implanted cancer cells without MSCs
into mice. To Karnoub’s disappointment, both groups’ tumors grew to
the same size and at the same speed.
But while the first group’s tumors
metastasized, the second group’s generally did not. Karnoub repeated this
experiment with several other lines of
human breast cancer cells and found
that others demonstrated similar
properties.
TUMOR IMAGE: ANTOINE KARNOUB; MICROSCOPY IMAGE : BENJAMIN ZESKIND
cancer cells, churning out about 60
times the normal amount. CCL5
is known to affect cell movement,
and its levels are elevated in the
blood of patients with advanced
breast cancer. Could the cancer
cells be “educating” the MSCs,
instructing them to make CCL5,
thereby promoting metastasis?
He tested this hypothesis by
coaxing weakly metastatic breast
cancer cells to produce lots of
CCL5 in the absence of MSCs.
These cells acquired the ability to
move and migrate to distant tissues, confirming CCL5’s key role
in MSC-moderated metastasis.
Karnoub found he also could halt
metastatic spread in the mice with
mixed tumors by simply blocking
CCL5 signaling.
Researchers at Brigham and
Women’s Hospital and Dana-Farber Cancer Institute then examined
CCL5 expression in tumor stroma
taken from breast cancer patients.
They found high CCL5 levels correlated with invasive tumors and
poor prognosis.
“MSC recruitment and CCL5
production could be responsible
for metastasis in a significant subset of breast cancer patients, which
has implications for diagnosing
and treating the disease,” Karnoub
asserts. “This protein sheds light
on how breast cancers mine the
body’s own resources to progress.”
– Alyssa Kneller
In mice, tumors recruit mesenchymal stem
cells (shown in green in a primary tumor)
from the bone marrow. Those cells create
a protein that helps tumor cells migrate.
x 10 -14
x 10 -14
1.5
1.5
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1.0
0.5
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Weigh cool
B
enjamin Zeskind set out to reveal
quantitative details about structures inside a living cell and
ended up with a new deep-ultraviolet
microscope.
“Traditional biological images are
mainly colorful pictures of cells and tissues that are limited to telling you if
something is present in the cell,” says
Zeskind. “We wanted to understand
better the structures in cells, how they
move around and change, so we needed
an inherent way of measuring how
much of a macromolecule is present in
the cell or an organelle.”
“When we started the project, people thought we were crazy,” he adds.
Now a Harvard Business School student, Zeskind was a biological engineering graduate student in Whitehead
Member Paul Matsudaira’s lab when he
led the development of the deep-ultraviolet microscope, which is described in
the July issue of Nature Methods.
Using the microscope at a deepultraviolet wavelength of 280 nanometers along with computational software
Zeskind developed, researchers can
analyze image intensity to determine
the mass of proteins and nucleic acids
in a cell. That gives a sense of how the
structures are distributed and how they
move and change over time.
“The nucleus of a cancer cell has
a very different structure from the
nucleus of a normal cell,” Zeskind
says. “This microscope helps us better understand the structures in cells
and their dynamics.” Down the road, he
suggests, the technique might lead to
advances such as very early diagnosis
of cancer.
These images of a mouse macrophage, taken
at 280-nanometer ultraviolet wavelengths,
show how the mass of proteins (left) and the
mass of nucleic acids (right) are distributed
in grams. As expected, nucleic acid is concentrated in the cell nucleus while proteins are
distributed more widely throughout the cell.
UV LEDs aid imaging
The microscope relies on deep-ultraviolet light-emitting diodes, a recent technology spin-off from the military that
can emit light at a precisely specified
wavelength and be switched on and off
rapidly. Zeskind took the glass lenses
out of a conventional light microscope
and installed quartz lenses (bought
used on eBay) to handle deep-ultraviolet wavelengths.
At those shorter wavelengths, the
UV microscope can provide more quantitative information as well as improve
the spatial resolution over that of a traditional light microscope.
The UV diodes also reduce the ultraviolet exposure and don’t kill the cell,
which has been the major challenge of
deep-ultraviolet imaging. The microscope can image cell division and migration for as long as 45 minutes with
minimal light-induced damage to the
cell. Deep-ultraviolet technology also
eliminates the need in traditional visible
light microscopy to label a cell with fluorescent dyes, which stress the cell.
“When Confucius said a picture is
worth a thousand words, he put a picture in the context of something else,
the number of words,” says Matsudaira,
who is director of the Whitehead-MIT
BioImaging Center. “This microscope
can give us a picture of a cell so we can
now ask how much protein is in it. It
allows us to think in a different way.”
– Lori Fortig
3
B
iology textbooks are blunt—
neutrophils are mindless killers. These white blood cells
patrol the body and guard against
infection by bacteria and fungi, identifying and destroying any invaders
that cross their path.
But new evidence, which may
lead to better drugs to fight deadly
pathogens, indicates that neutrophils might actually distinguish
among their targets. A scientist in
the lab of Whitehead Member Gerald
Fink has discovered that neutrophils
recognize and respond to a specific
form of sugar that comprises just a
small fraction of the fungal cell wall.
“We showed that neutrophils
respond in a completely different way to slight changes in sugar
composition,” explains Whitehead
postdoctoral researcher Ifat RubinBejerano, first author on the paper,
which appeared online in July in the
journal Cell Host & Microbe. “If we
are able to use this unique sugar to
excite the immune system, it may
help the human body fight infection.” She cofounded a company
called ImmuneXcite to explore this
possibility.
– Alyssa Kneller
Neutrophils (shown in pink) recognize and
respond to a particular form of sugar contained on the surface of pathogenic fungi.
4
The team reporting a new way to detect DNA damage includes MIT professors Linda Griffith,
Leona Samson, and Harvey Lodish; and chemical engineering student Joe Shuga.
Test could aid drug development
R
esearchers from Whitehead and
MIT have developed a cell culture test for assessing a drug
compound’s genetic toxicity that may
prove dramatically cheaper and more
efficient than existing animal tests.
Like the current FDA-approved
test, the new test looks for DNA
damage in red blood cells formed in
the bone marrow of mice. The precursors to red blood cells are handy
for this because such cells normally
lose their nucleus during the last stage
of red cell formation, and DNA-damaged precursors generate red blood
cells containing an easily detected
“micronucleus” consisting of fragments of nuclear DNA.
Unlike the current procedure,
which injects the compound into a
live mouse, the new assay is a cellculture system that could allow hundreds or thousands of tests to be
performed from the bone marrow of
a single mouse, and potentially from
human bone marrow.
Joe Shuga, who developed the
assay, was a graduate student in the
labs of MIT professors Linda Griffith,
Harvey Lodish (a Whitehead Member) and Leona Samson. Griffith is
senior author on the paper, published
in the Proceedings of the National
Academy of Sciences in May.
Shuga first worked with postdoctoral researcher Jing Zhang in the
Lodish lab to adapt techniques from
an established cell-culture system
based on mouse fetal liver cells to create a new system based on adult red
cell precursors from mouse bone marrow. Shuga patiently optimized the
system, which allows the precursor
cells to proliferate and differentiate in
the normal way, dividing four or five
times before losing their nucleus and
becoming immature red blood cells.
He then studied the way these
developing cells reacted to three toxic
DNA-damaging agents and found the
results correlated well with results
from the existing test. He further confirmed the results in experiments with
mutant mice created by Samson’s lab
that are deficient in certain DNArepair systems.
With the new assay, “instead of
testing one chemical and one dose in
one animal, you’ll be able to take one
animal, get the bone marrow out and
test a thousand different conditions,”
Samson says.
“And although we haven’t done
it,” adds Lodish, “you may be able to
extend the technique to humans.”
– Eric Bender
ILLUSTRATION: TOM DICESARE; PHOTOGRAPH: DONNA COVENEY/MIT
science digest
White blood
cells are picky
about sugar
Some microRNAs may
help prevent tumors …
JOHN SOARES
A
microRNA directly
regulates a gene
implicated in
human cancers, Whitehead
researchers reported in
February in Science.
MicroRNAs are tiny
snippets of RNA that can
repress gene activity by
targeting the gene’s messenger RNA (which copies DNA information and
starts the process of protein production).
Many microRNAs
have been found in diverse
plants and animals, and
there are hundreds in
humans. In fact, microRNAs regulate over a third
of the human genome, as
shown in a 2005 study
by the lab of Whitehead
Member and Howard
Hughes Medical Institute
Investigator David Bartel
and colleagues.
But given the wealth
of microRNAs, and the
ability of individual microRNAs to target hundreds
of genes, researchers have
struggled to show the biological impact of a particular microRNA on a
particular target in mammals (although such connections have been shown
in plants, worms and flies).
Several groups have demonstrated that over-expression or under-expression
of a microRNA can play
a role in certain cancers,
but no one has clarified the
genes responsible.
Looking to find a
promising target for an
individual microRNA,
Christine Mayr, a postdoctoral researcher in the Bartel lab, picked Hmga2, a
… while others may
trigger metastasis
T
gene that is defective in
a wide range of tumors.
It turns out that in
its non-protein-producing region, Hmga2 has
seven sites that are complementary to the “let7” microRNA, which
is expressed in the later
he jury is in:
microRNAs can
cause tumors to
metastasize, prompting
otherwise sedentary cancer
cells to move and invade
other tissues.
Working in the lab of
Whitehead Member Rob-
Christine Mayr pinpointed
the role in mice of a single
microRNA in regulating certain
kinds of cancer.
Li Ma demonstrated that overabundance of a single microRNA
can cause tumors to spread to
distant tissues in mice.
stages of animal development. Mayr found clear
evidence, both in cell cultures and in mice, that
let-7 is involved in regulating Hmga2, and that disrupting let-7’s ability to
repress Hmga2 would lead
to tumor creation.
The results highlight a
new mechanism for cancer
formation and show that
the interaction of a single
microRNA with one of its
target genes can produce a
certain trait in mammals.
“Seeing this encourages us
to explore the biological
importance of other examples of microRNA regulation,” says Bartel.
– Eric Bender
microRNAs were involved
in any biological process,”
says Weinberg.
Ma found that
one microRNA called
microRNA-10b appeared
in high levels in metastatic
cancer cells.
Next, she forced nonmetastatic human breast
cancer cells to produce
lots of microRNA-10b by
inserting extra copies of
the gene.
She injected the altered
cancer cells into the mammary fat pads of mice,
which soon developed
breast tumors that metastasized.
Ma then used a program developed in the
Bartel lab to search for the
target of microRNA-10b.
One target was the
messenger RNA for the
protein HoxD10, which
can block the expression
of genes required for can-
“This encourages us to explore the biological
importance of other examples of microRNA
regulation.” - DAVID BARTEL
ert Weinberg, postdoctoral
fellow Li Ma has coaxed
cancer cells to break away
from a tumor and colonize
distant tissues in mice by
simply increasing the level
of one microRNA.
Her results appeared
online in Nature in September.
“Li has shown that a
specific microRNA is able
to cause profound changes
in the behavior of cancer
cells, which is striking
considering that 10 years
ago no one suspected
cer cells to move.
When Ma boosted the
level of HoxD10 in cancer
cells via artificially high
levels of microRNA-10b,
the cells lost their newly
acquired metastatic
abilities.
“During normal development, this microRNA
probably enables cells to
move from one part of the
embryo to another,” adds
Weinberg. “Its original
function has been co-opted
by carcinoma cells.”
– Alyssa Kneller
5
What do university students need to know about biology?
How is the teaching of biology
changing?
What has really emerged in the last
twenty years is the sense that biology isn’t an isolated subject. That’s
certainly been recognized since the
dawn of molecular biology in the ’40s
and the ’50s, but that sense really did
not permeate biology education for
a while. And what’s happened, and
How can you best teach such a vast
and rapidly growing subject?
That’s an interesting question. We
teach one semester of introductory
biology, and what I do in my course
is get rid of all history. There’s what
we know, and what we’re trying to
know, and what the current challenges are.
But we touch on a very small part
of biology in our course. And there
is a real question as to whether it’s
enough. We’ve thought about having a second semester, elective rather than
Whitehead Member
Hazel Sive, who was
required, that would
appointed associate
be advanced introducdean of MIT’s School
tory biology.
of Science this summer,
considers how we teach
life sciences now—
and what’s coming.
what’s happening, is that the connection between biology and the other
disciplines has become very strong.
Biology has permeated every other
topic at MIT.
There are very strong intellectual
bridges, research bridges and teaching bridges built between biology and
other departments. This is a trend
that only will strengthen.
In the future, you may not come
to MIT to study biology per se. It
may be that you will come here to
study biophysics or biochemistry or
bioethics. You will focus more on
specific areas of biology because biology itself is so big.
6
Why should every MIT
student learn about
biology?
There are a few good reasons that
biology is a general Institute requirement.
One is that the current estimate is
that 40 percent of all MIT research is
biology-based. So the students who
sit in my class need the background.
And I’ll make a prediction that 70
percent of our students will, at some
point, do something in their careers
that touches on biology, no matter
what major they take.
Another part is that the moment
they become MIT students they are
spokespeople for science, within
their own families and within their
own communities. People will ask
them questions, and they need to be
informed.
And then I always throw in for
my students that this is really cool
stuff, and this is about you. It’s fascinating to think that you came from a
single cell.
What do undergraduates learn in
the lab?
Eight-five percent of our students participate in lab research at some point
during their three years as biology
majors. Those students get training
in how to design experiments, how
to test hypotheses, how to think logically in a practical kind of way. It’s a
very powerful program.
Students are strongly encouraged
to stay in a lab for a minimum of two
semesters, or a summer and a semester. We really encourage students
to go deep into one lab rather than
to get a smattering of how things
work. The idea is to learn how to
do research, and you can’t do that if
you’re just sampling. We want them
to get into the kitchen and figure out
how to make the food on the table,
not just arrange it on the plate and
maybe eat some of it.
Are methods of teaching changing?
For me, the one-on-one conversation,
without any electronic devices, except
to augment information, is the heart
of pedagogy, and I never want that to
change.
The Internet clearly can, and has
done, an enormous amount of good.
It’s so easy to look something up
now. It used to be so arduous. And
that’s fantastic. It helps with my lectures; it lets my students get to know
what’s out there.
But I’m a believer in using information to help thinking, not substituting information from the Internet.
I have a radical idea for MIT: we
turn off the Internet for three hours a
day. That would encourage our students, especially our undergraduates,
to go back to old-fashioned mechanisms of communicating that involve
conversations and sitting down and
thinking things through in a quiet
manner that is not intruded upon
by music or flashing things or other
input from the Internet.
Are we recruiting the right number of
students to do biomedical research?
One does look at the huge number
of buildings going up, and wonder
where all those research scientists will
come from, and what they’ll do, and
who will fund them. On the other
hand, there’s a lot of information that
needs to be gathered, and we need
people to gather it.
FURNALD/GRAY
fast FAQs
Learning about life
Scientists from David Sabatini’s
lab gather in an MIT gym.
PUMPING UP
RESEARCHERS PROBE THE DIVERSE ROLES OF mTOR PROTEINS
IN GROWTH, CANCER AND BODYBUILDING
By Alyssa Kneller
photograph by john soares
7
through a fitness magazine purchased as a gag
gift when an ad catches their attention. A mas-
sive bodybuilder in a tank top stands behind a lab bench
with a distinguished-looking man in a white lab coat.
“Genetic limitations are a thing of
the past,” reads the headline. “Anator-p70 turns on the three major
muscle-building master genetic regulators, mTOR, PKB, and p70S6K.”
“We’ve been scooped,” joke the
two graduate students, who work in
Whitehead Member David Sabatini’s
lab, which is largely devoted to the
study of mammalian TOR (mTOR).
This protein serves as a kind of traffic
cop, allowing cell growth and proliferation to proceed when amino acids
and growth factors are abundant
and blocking these processes when
nutrients are scarce. But how nutrients regulate mTOR signaling to control size remains a major mystery—to
academic scientists, anyway.
According to the ad, Anator is the
culmination of five years of research
by Team MuscleTech and represents
a “scientific breakthrough the likes
of which the supplement world has
never before seen.” The product purports to activate mTOR and other
growth regulators with special ingredients called LeuciGene, PhenylGene
and GeneTOR. The ad even includes
a diagram of the mTOR signaling
pathway to illustrate how these ingredients work.
Had Team MuscleTech solved the
mystery that has eluded Sabatini and
other mTOR experts for a decade?
Had the supplement creators parsed
out some missing players upstream of
mTOR and unlocked the black box
of nutrient sensing?
Probably not.
A close examination of the Anator label reveals that “LeuciGene”
contains several derivatives of the
amino acid leucine, which is already
known to activate mTOR. Just to
be safe, Sabatini lab technician Robert Lindquist hikes down to the local
GNC and asks for some Anator. The
8
salesman announces he’s in luck. A
shipment has just arrived.
Back at Whitehead Institute,
Lindquist and several of his equally
lean colleagues engage in a brief
workout and then prepare Anator
shakes in the third-floor lounge. In
addition, graduate student Yasemin
Sancak tests the product on cells in
culture. Results: Anator does activate
mTOR, but the amino acid leucine
works just as well.
What a relief!
“I’ve used this pseudoscience in
talks to joke with competitors, and
some do start to look nervous until
they see the ad,” says Sabatini.
Sabatini has devoted much of
his career to TOR. At Johns Hop-
ists had teased apart the details of the
Krebs cycle and other major metabolic pathways.
In essence, the discovery of
mTOR’s function stirred up a stagnant area of research, prompting scientists to reexamine how cells and
organisms use energy and nutrients to
grow (and providing fodder for protein supplement marketers).
“Our work brings us back to one
of the most interesting, and obvious,
questions out there,” says Sabatini.
“How does biology regulate size?”
As it turns out, mTOR is likely
involved at all levels, regulating size
for cells, organs and organisms. Drosophila and mice with low levels of
mTOR signaling are much smaller
than usual. Their constituent cells are
also smaller.
Thus mTOR research could eventually explain why organs change size
in response to environmental cues or
why mice are so much smaller than
humans, despite the fact that we
share thousands of the same genes. It
could also provide new insights into
“OUR WORK BRINGS US BACK TO ONE
OF THE MOST INTERESTING, AND
OBVIOUS, QUESTIONS OUT THERE:
HOW DOES BIOLOGY REGULATE SIZE?”
– DAVID SABATINI
kins in the mid-1990s, he led one of
the teams that discovered the mammalian version of the protein while
working on rapamycin, a drug that
helps prevent organ rejection in transplant patients. Sabatini found that the
drug works by blocking a previously
unknown protein, which was eventually dubbed mTOR (for mammalian
target of rapamycin).
Supersize me
abs soon showed that mTOR
serves as an important signaling
hub, using information about the
environment to regulate cell growth.
This surprised many scientists, who
assumed that all the major mysteries of metabolism had been solved by
the 1930s, at which point biochem-
L
diseases such as diabetes, which is
characterized (in part) by abnormal
metabolism.
A cellular relay race
hink of mTOR as the anchor runner in a complex relay race. It
cannot sense nutrients and growth
factors directly. Instead, it relies on
other proteins, or runners, to gather
information from the cellular environment and pass it along like a
baton. Each baton changes hands a
number of times before ending the
race at mTOR. Given the right combination of batons, or signals, mTOR
recognizes that conditions are optimal for growth and instructs the cell
to make more proteins.
Over the past 10 years, Sabatini’s
T
PREVIOUS PAGE: PHOTOGRAPHED AT ALUMNI POOL & WANG FITNESS CENTER
mTOR proteins
S
homit Sengupta and Jan Reiling are flipping
JUSTIN KNIGHT
Once his lab demonstrated that mTOR activates the prominent cancer protein Akt, many
labs and pharmaceutical companies began
following up, says David Sabatini.
lab has identified some of the runners
and batons, though many remain a
mystery. In 2002, for example, DoHyung Kim (now a faculty member
at the University of Minnesota) published a paper in Cell showing that
mTOR typically sidles up to a protein
called raptor. Without this essential
binding partner, codependent mTOR
loses its ability to sense nutrients and
promote growth.
More recently, graduate students
Yasemin Sancak and Carson Thoreen
discovered that a protein called
PRAS40 lounges on raptor, keeping
mTOR’s binding partner in check.
But it springs out of the way when
levels of the hormone insulin rise.
Insulin circulates through the body
when an animal is well fed, instructing cells to absorb and store glucose.
Thus PRAS40 allows raptor and
mTOR to foster protein production
when nutrients are abundant.
“The intricacies of this particular
pathway are astonishing,” says Sancak. “And we’re just beginning to
appreciate how mTOR interacts with
a myriad of other pathways related to
cell growth,” adds Thoreen.
The cancer connection
abatini’s lab dropped a bombshell in February 2005, when it
reported on an unexpected role for
mTOR in the journal Science. Dos
Sarbassov, now a principal investigator at the University of Texas Medical
School, showed that mTOR activates Akt, a prominent cancer protein
involved in cell proliferation.
Researchers had overlooked this
connection because they had focused
on raptor, which enables the drug
rapamycin to target mTOR. Scientists
didn’t realize that mTOR sometimes
“cheats” on raptor by cozying up to
a different protein called rictor. When
mTOR binds to rictor, it generally
becomes immune to rapamycin, and
assumes different functions.
“The first TOR complex regulates the size of a cell, while the second regulates cell division and cell
survival,” explains postdoctoral
researcher David Guertin. “Both
S
complexes use information from the
cellular environment to make decisions about growth, but the function
of the second complex may be more
closely linked to human cancers.”
Sarbassov relied on biochemical
techniques to interfere with mTOR
in a Petri dish, so some scientists
remained skeptical of its cancer-causing role in animals. Guertin erased
their doubts by knocking out rictor
in mice and showing that Akt activity dropped significantly. His results
appeared in Developmental Cell in
December 2006.
“The discovery greatly increased
the interest in the field, because many
tumors exhibit deranged Akt signaling,” says Sabatini. “Many labs and
pharmaceutical companies are now
searching for ways to inhibit the second mTOR complex.”
Sabatini lab researchers are tackling this problem too. But they’re
thinking more holistically about the
connection between metabolism and
cancer. Scientists have known for
decades that animals live longer and
develop fewer tumors when they’re
fed low-calorie diets. mTOR may
offer a mechanistic explanation.
“Research on mTOR in mice
could help us connect the dots
between metabolism and cancer,”
explains postdoctoral researcher
Nada Kalaany. “We may have found
the missing link.”
And it turns out that the two pathways involving mTOR intersect. The
rictor/mTOR complex runs before the
raptor/mTOR complex in the giant
cellular relay race. Thus the pathway
that pumps you up by increasing cell
mass coordinates with the pathway
that controls cell division.
“I never thought that the work
on rapamycin would lead to a new
field,” remarks Sabatini. “It’s been
gratifying for me to be part of something that is having an important
impact on both our basic understanding of biology and our treatment of
disease.”
9
CELLS CREATED FROM
SCRATCH TO TRIGGER
BREAST CANCER
WILL BRING NEW
EVIDENCE TO A FIERCE
SCIENTIFIC DEBATE
By Alyssa Kneller
10
Like fashion, science sometimes
travels in circles. A model of cancer
proposed in the 1800s has recently
returned to vogue, with huge implications for how we diagnose and treat
this group of deadly diseases.
During the 19th century, pathologists noticed that under the microscope, some tumors resemble
embryonic tissues: both contain many
rapidly dividing cells that appear
to be disorganized. By 1875, Julius
Cohnheim and Francesco Durante
had proposed that tumors arise from
embryonic remnants in adult tissues.
They planted the seeds for the
modern hypothesis that tumors are
driven by a rare population of stem
cells that can both regenerate themselves indefinitely and give rise to
other kinds of cells. But their ideas
went out of fashion in the last half
of the 20th century with the rise of
a competing model of cancer called
clonal evolution.
Under this egalitarian model, all
cancer cells possess equally destructive potential. Although cancer cells
are heterogeneous, all or most of
them have the capacity to create a
new tumor. A cell becomes cancerous
after acquiring a series of mutations,
and descendants of that original miscreant evolve while competing with
one another for resources. Thus,
given the right combination of genetic
alterations, any cancer cell can trump
its neighbors, expand its territory
locally and colonize distant tissues.
Some recent discoveries, however, support the hierarchical model
of cancer, in which a handful of stem
cells reign supreme. These despots—
which become cancerous through a
TAN INCE
Shedding light
on cancer stem cells
series of mutations—retain control
over their descendants, which form
the bulk of a tumor. Unlike their offspring, cancer stem cells can live
indefinitely and seed new tumors.
The cancer stem cell hypothesis could explain why tumors often
return after patients receive chemotherapy or radiation. Such treatments
may spare the slow-growing, unspecialized cells at the root of the tumor.
Unsurprisingly, this hypothesis has kicked off an enormous
uproar among cancer researchers.
Recent work at Whitehead, allowing
researchers to create cells that trigger
breast cancer in mice, should help to
clarify this puzzle.
Solid tumor evidence
The modern retelling of the story
begins with Michael Clarke, stand-
ing before a room full of medical students at the University of Michigan
and delivering a lecture on testicular cancer. The professor of internal
medicine made an observation that
changed his career: the tumor tissue
displayed on the screen above held
only a few immature cells surrounded
by countless specialized cells.
“That was the eureka moment,
when I suspected that solid tumors
have stem cells in them,” he recalls.
Although John Dick of the University of Toronto had isolated cancer
stem cells from leukemias in the mid1990s, most scientists assumed they
were unique to blood cancers.
But Clarke began hunting for
these elusive entities in human breast
tumors, aided by the recent discovery that normal adult stem cells typically express telltale CD44 proteins
Left, sheets of normal human breast cells
(whose membranes are stained red) have been
grown in a new culture medium. Right, the
normal cells have been transformed into cancerous cells (with membranes stained green).
As many as one in ten are cancer stem cells.
on their surface. For months, Clarke
hovered near a cell-sorting machine
with postdoctoral fellow Muhammad
Al-Hajj, sifting through cancer cells
in search of the right protein patterns.
Eventually, Clarke and his colleagues at the University of Michigan
succeeded in isolating a population
of potent tumor-initiating cells that
were dotted with CD44 proteins,
yet were missing the CD24 proteins
that were typical of more specialized cells. When Al-Hajj injected the
breast cancer cells into mice whose
immune systems were compromised,
11
Hitting the trifecta
Taken alone, any one
of these three discoveries would fail
to generate dozens
of reviews. The term
“cancer” encompasses a multitude of
diseases characterized by the abnormal proliferation of
cells, so the presence
of stem cells in a particular type of tumor
doesn’t mean much.
In combination,
however, the studies
suggest a paradigm
with enormous clinical ramifications.
“The reason the
cancer stem cell hypothesis has taken
so much of my time is because of the
potential implications for therapy,”
says University of Toronto’s Dirks. “It
appears that cancer stem cells resist
conventional treatments, so we need
to find a way to target them.”
Chemotherapy can resemble
the arcade game Whac-A-Mole, in
which players use a mallet to hit plastic moles that pop up from different
holes. The game is seemingly futile, as
the moles continue to surface—sometimes in the same spot—after being
hit. Similarly, chemotherapy kills
many cancer cells and causes tumors
to shrink, but they often return after
a few months.
What’s a cancer stem cell?
“The descriptions of a cancer stem cell are as diverse
as the labs working in this
field,” says Whitehead visiting scientist Tan Ince.
In the strictest sense,
a cancer stem cell is a rare
undifferentiated tumor cell
that’s uniquely capable of
renewing itself and seeding new tumors. Under this
interpretation, cancer stem
cells drive tumor growth (by
12
giving rise to the differentiated cells that form the bulk
of the tumor) and initiate
metastasis. They also resist
conventional radiation and
chemotherapy, which could
explain why many tumors
relapse after treatment.
Many scientists suspect that cancer stem cells
come from normal adult stem
cells, though this remains
unproven.
Cancer stem cells
remained hidden for
decades because scientists couldn’t distinguish
them from their descendants. Advances in cell sorting techniques and detailed
characterizations of adult
stem cells finally made it
possible to isolate cancer
stem cells from tumors. But
few labs possess the expertise, equipment or patience
to sort and expand the elusive cells.
Striving to create better models of breast
cancer cells, Tan Ince (above) ended up producing cancer stem cells. Other labs can easily grow the newly created cells for their own
experiments, notes Robert Weinberg (right).
That may be because cancer stem
cells resist conventional chemotherapy drugs and “rebuild” after their
descendants die, explains Dirks.
Studies in leukemia support this
hypothesis. For example, Tessa Holyoake, a professor at the University of
Glascow, has discovered a mechanism
by which blood cancer stem cells
keep the drug Gleevec at bay. The
stem cells have proteins on their surfaces that prevent this potential killer
from accumulating inside by literally
pumping it out.
Duke University’s Jeremy Rich has
shown that some cancer stem cells
also resist radiation treatment. When
he exposed brain cancer stem cells to
radiation, they cleverly shifted DNA
damage repair activities into high
gear, thereby dodging destruction.
Scientists are trying to disable
these coping mechanisms and find
other ways to kill cancer stem cells
to prevent tumors from returning. In
May, Dirks published the results of a
chemical genetic screen, which uncovered several small molecules that
inhibit cultures enriched for brain
cancer stem cells.
SAM OGDEN
cancer stem cells
they developed tumors—and they
did so after only 100 cells had been
introduced instead of the hundreds
of thousands that would typically be
required to achieve the same effect.
The discovery of cancer stem
cells in human breast tumors, which
appeared in Proceedings of the
National Academy of Sciences in
2003, reinforced Dick’s findings.
“I ignored the discovery of cancer stem cells in leukemias because
I thought they might be an idiosyncrasy of blood cancers,” comments
Whitehead Member Robert Weinberg. “But when Michael Clarke’s
laboratory published compelling evidence of cancer stem cells in breast
tumors, I took note.”
Now a professor at Stanford,
Clarke is not the only scientist to
find himself unexpectedly at the center of the controversy over cancer
stem cells. Though journals have
published dozens of reviews on the
topic since his discovery, just a handful of labs have produced solid data
that advances or challenges his findings, but they have all attracted considerable attention. Peter Dirks of the
University of Toronto, for example,
entered the spotlight in the cancer
research community by isolating stem
cells from brain cancer in 2004.
Since then, stem cells have continued to pop up in other types of solid
tumors. For instance, Clarke and his
colleagues pulled them from colon
tumor tissue this spring.
“Looking ahead, we need to
build our knowledge of cancer stem
cells into the drug discovery process,”
says Dirks.
In addition, the cancer stem cell
hypothesis may change the way cancer is diagnosed. In a New England
Journal of Medicine paper published
in January, Clarke and his colleagues
demonstrated that the level of expression of 186 genes in cancer stem cells
can predict the risk of recurrence in
patients with breast cancer, lung cancer and a type of a childhood brain
cancer. By isolating cancer stem cells
from tumor tissue, he discovered useful information about the stage of the
disease.
“As far as I know, this is the first
time that the isolation of cancer stem
cells has been shown to directly have
clinical applications,” says Clarke.
SAM OGDEN
Which cancers, when?
But scientists caution against tossing out existing cancer paradigms and
tools before they acquire more data.
For example, neither Clarke nor Dirks
is convinced that the cancer stem cell
model applies to all types of cancer.
Associate professor Kornelia
Polyak of Harvard Medical School
and Dana-Farber Cancer Institute
couldn’t agree more. Polyak was
intrigued by Clarke’s 2003 discovery of breast cancer stem cells, but
instead of publishing a review, she
decided to test his results.
Her findings, which appeared
in Cancer Cell in March, match
the clonal evolution model of can-
cer, rather than the cancer stem cell
hypothesis. She discovered that the
descendants of the cancer cells with
stem cell properties continue to
undergo genetic evolution, which suggests that they too can drive tumor
progression.
“I do believe there are cells in a
tumor that have the features of stem
cells and that those cells are more
invasive and metastatic than their
more differentiated counterparts,”
says Polyak. “But I don’t think they’re
always rare, and I don’t think they’re
the only cells responsible for tumor
recurrence and drug resistance.”
If this were the case, she says, then
recurrent tumors, presumably composed of the descendents of cancer
stem cells, would be sensitive to the
same treatment as the original tumor,
and acquired drug resistance would
never occur.
It’s possible, says Polyak, that
mice may have misled Dick, Clarke
and Dirks. Mice may provide a hostile environment for differentiated
cancer cells that are fully capable of
initiating tumors in humans in the
right environment.
Scientists clearly need more data
to resolve these issues, but just a
handful of labs have the tools and
resources to isolate and grow the elusive cells.
Cancer stem cells on call
That could change thanks to Whitehead visiting scientist Tan Ince,
who recently created breast cancer
stem cells from scratch. His findings
appeared in Cancer Cell this August.
He didn’t set out to engineer
these potent cells. As a postdoctoral
researcher and pathologist in the
Weinberg lab, Ince was simply trying
to create breast cancer models that
look like real human tumors under
the microscope and behave like those
seen in many patients.
Ince developed a recipe for a
chemically defined culture medium
and managed to grow a type of normal human breast cell that ordinarily dies in culture. He transformed it
into a cancer cell by inserting specific
genes through a standard procedure.
The engineered cells proved to
be extremely powerful. When Ince
injected more than 100,000 of them
into a mouse with a compromised
immune system, the mouse quickly
developed massive, deadly tumors. In
initial experiments, a few tissue slices
revealed a primary tumor structure
that resembled that of cancer patients
with metastases.
That prompted Ince to wonder
whether the cancer cells he created
would metastasize if the mouse lived
longer. He repeated the experiment in
other mice, reducing the number of
cells in the injection to as few as 100
in hopes of slowing tumor growth.
The cancer cells continued to seed
tumors and the tumors metastasized.
After submitting the work for review,
Ince even generated tumors with an
injection of just 10 cells.
“In the process of making a model
that reflects a tumor type common
in patients, I created tumor-initiating
cells,” says Ince, now an independent
investigator at Brigham and Women’s
Hospital and an instructor at Harvard Medical School. “That was a
complete surprise.”
“This work could provide a boon
to researchers who study these elusive
cancer stem cells by offering a bountiful source of them,” says Weinberg.
“Labs can easily grow the newly created cells for use in experiments.”
The cells provide a common platform for discovery. The field can
progress more quickly with many
researchers working on identical
cell lines and repeating each other’s
experiments. The cell lines will also
make it possible for labs to jump into
the field without learning the tedious
and expensive cell-sorting techniques
required to isolate cancer stem cells
from tumors.
“It’s currently very difficult to isolate and expand cancer stem cells
from patients, so researchers are
reluctant to share them with other
labs, but we’ve circumvented this barrier,” says Ince. “At some point, scientists need to stop writing reviews
and start doing experiments to
advance the debate, and this platform
will help them do that.”
13
The human side of monkeypox
IN THE CONGO, KATE RUBINS AND COLLEAGUES
STUDY THE SMALLPOX-LIKE DISEASE By Eric Bender
The single-engine plane
lifted off the runway and
up through the smog over
Kinshasa, loaded near its
maximum weight with five
people, a portable lab isolation hood and related gear.
In mid-July, Kate Rubins
and her colleagues were
headed for Kole, a remote
and poverty-stricken village five hours by air from
the Democratic Republic of
Congo’s capital.
There, in a mission hospital, they would spend
several weeks gathering blood samples from
patients with monkeypox.
Like smallpox, monkeypox is a poxvirus, equipped
with only about 200 genes
but cunningly crafted for
attack. “It’s a tiny bit of
1
nucleic acid and a few proteins all wrapped up, and it
can kill you,” says Rubins,
a Whitehead Fellow.
While episodes of monkeypox are reported sporadically, Rubins and her
colleagues believe it is
endemic in this isolated
area of Africa. Villagers
most likely get the disease
by eating or being bitten by infected monkeys
or rodents. Monkeypox is
less dangerous to humans
than smallpox and less easily transmitted, but it kills
about 10 percent of its victims, and may leave others
2
3
4
1. In the Kole hospital, “the walls
are crumbling and the glass
panes are falling out–and it’s one
of the best-maintained hospitals
in that part of that country,” notes
Kate Rubins. The central African
country is plagued by violence.
14
2. Some patients walk dozens of
miles to be admitted to the hospital, which treats an increasing
number of monkeypox patients
every year.
3. An expert on dangerous
viruses, Rubins is no stranger to
Biosafety Level 4 laboratories.
The lab at the Kole hospital was
at the opposite extreme, like “a
microbiology lab from 1910.”
4. The only lights in the lab came
from the scientific equipment,
notably this portable lab isolation hood. Power came from solar
power or generators, but half the
time there was none.
blind or permanently disfigured. The hospital treats
patients with intravenous
fluids and antibiotics for
secondary infections.
Monkeypox first
appeared in the medical literature several decades ago,
but “it’s like a new disease
because it’s so understudied,” says Rubins, whose
team collaborated with
the Congolese Ministry of
Health.
Other collaborators
include Emile Okitolonda
Wemakoy of the Kinshasa
School of Public Health,
Jean Jacques Muyembe–
Tamfum of the National
Institute of Biomedical
Research in Kinshasa, Anne
Rimoin of the University
of California/Los Angeles
School of Public Health,
David Relman of Stanford
University and Lisa Hensley and John Huggins of
the U.S. Army Medical
Research Institute of Infectious Diseases. Funding
came from USAMRIID, the
Pacific Southwest Regional
Center of Excellence for
Biodefense and Emerging
Infectious Disease, and the
National Academies Keck
Futures Initiative.
While the team was in
Kole, the researchers separated patient blood samples
into many different components. This work was
done in the field because
the samples had to be
processed fresh and then
stored in liquid nitrogen.
The scientists are now
examining how monkeypox affects various components of the human
immune system, including innate immunity (the
first line of defense against
invaders), cytokines (which
aid in many immune cell
processes, such as help-
5
6
COURTESY OF KATE RUBINS
8
5–7. Monkeypox lesions break out on the face, limbs and hands, and
last about three weeks. Medical staff drew the lines on this boy’s face
to help track the lesions. There is no drug regimen for the disease, but
patients generally do better in the hospital.
ing to tailor T-cells to handle a given pathogen), and
antibodies, which recognize and destroy infectious
organisms.
This basic research will
help in developing vaccines
and drugs for monkeypox
and smallpox. “It’s amazing to discover the inner
workings of this cousin
of humankind’s deadliest
plague, but also to be making some small impact on
this remote corner of the
globe,” Rubins says.
Kelli Whitlock Burton contributed to this story.
7
9
8. Patients go to the monkeypox
isolation ward when they develop
lesions. Often patients have great
difficulty swallowing and become
dehydrated.
9. “People in the village were fantastic,” says Rubins. About half
the village’s population greeted
the research team’s plane, and
the team’s work drew a constant
stream of onlookers.
15
This mouse grew from an
embryo containing adult cells
that had been reprogrammed
to an embryonic state. Marius
Wernig (left) and Alexander
Meissner were among five lead
authors on the Nature paper.
Break no eggs
BEHIND THE SCENES OF AN ASTONISHING LEAP IN EMBRYONIC STEM CELL SCIENCE
By David Cameron
photographs by sam ogden
16
17
The young Austrian scientist was
determined to devote his entire career
to solving one of biology’s most fundamental and difficult questions.
Unfortunately, he wasn’t sure what
that question was.
“All I knew for certain was that
I did not want to spend my life making small contributions to areas
we already knew lots about,” says
Hochedlinger, a faculty member at
Harvard Medical School whose lab
is at Massachusetts General Hospital (MGH). “I wanted to pursue an
aspect of biology that was absolutely
new—and vital.”
But finding the next big thing
before it gets big requires not only
ambition but a generous helping of
luck. Fortunately for Hochedlinger,
luck struck.
One day in 1999, he attended a
packed university lecture by Whitehead Member Rudolf Jaenisch. The
message couldn’t be clearer: In the
world of developmental biology,
everything had changed.
Three years earlier, Dolly the sheep
had been cloned, a feat that contradicted the scientific mainstream
thinking of the time. Dolly was created through a process called nuclear
transfer, in which the nucleus from a
single skin cell was inserted into an
egg that had been stripped of its own
This is your brain
Well, no. The above cells are
motor neurons, the nuts and
bolts of your central nervous
system. But these particular
human cells will never have
18
nucleus, and then coaxed into develming, including the first proof-inoping into an embryo. Dolly was the
principle in mice of using somatic cell
genetic twin of the sheep that had
nuclear transfer for therapeutic purdonated the skin cell.
poses. In 2005 he left to start his own
But how did this happen? How
lab at MGH.
did the egg take a fully mature cell
Then came the shocker.
and send it back down its ancestral
A tale of four factors
lineage to that develFor embryonic stem cell
opmental moment
research, 2006 was the
when it was once
best of years and the
again a blank slate,
worst of years.
devoid of all memories
The best came at a
of ever having been
meeting of the Internaskin?
tional Society for Stem
What, exactly, was
Cell Research in June
going on inside that
2006, when Shinya
skin-cell nucleus as
Yamanaka of Kyoto
the egg turned back
At Whitehead, Konrad HochedUniversity reported that
the clock and reprolinger studied how, in cloning,
it’s possible to take a
grammed it into an
an egg reprograms the nucleus
mature mouse skin cell
embryo?
of an adult cell.
and do with it exactly
That, Jaenisch told
what the scientists had
the audience, was one
done with the donor cell that created
of the great biological questions of
Dolly a decade earlier.
our time.
Without the egg.
“I knew immediately that I was
Through long and arduous
going to devote my career to answering that question,” says Hochedlinger. genomic screenings, Yamanaka had
Hochedlinger moved to the United found four genes belonging to a category called “transcription factors”
States and joined Jaenisch’s lab at
that were excellent candidates for
Whitehead Institute, first as a graduate student and then as a postdoctoral reprogramming a cell. These factors—Oct4, Sox2, c-Myc and Klf4—
researcher. He was a lead author on a
are gene master regulators, meaning
number of key papers that explored
that they preside over large groups of
the dynamics of nuclear reprogram-
the pleasure of helping someone walk, swallow or breathe.
Instead, these motor neurons started out as human
embryonic stem cells and
were subsequently cultivated
into the cells at left by Maya
Mitalipova, a member of the
Jaenisch lab and director of
Whitehead’s human embryonic
stem cell facility.
Growing neurons out of
human embryonic stem cells
is an extraordinary feat in
itself, but a team consisting of
Whitehead Members Rudolf
Jaenisch and Richard Young
and Affiliate Member David
Gifford plans to do far more
than that. In collaboration with
Columbia University neurobiology expert Thomas Jessell,
the team received a five-year,
$6.8 million grant last year
to unpackage the molecular strategies that cells use to
graduate from the “be all you
can be” embryonic stem cell
to one of the most specialized
human cells: the neuron.
Team members believe
that prying open each step of
this process will yield insights
into certain motor-neuron diseases, such as amyotrophic
lateral sclerosis (Lou Gehrig’s disease) or spinal muscular atrophy. “So far these
diseases have been hard to
understand because of our
sketchy information on the
normal molecular profile
of motor neurons,” says
Jessell. “We plan to change
that.”
– David Cameron
CELL IMAGE COURTESY OF MAYA MITALIPOVA
embryonic stem cells
As an undergraduate at the Institute for Molecular Pathology in Vienna, Konrad Hochedlinger was thinking big.
genes. Manipulating any factor results
in a cascading effect through any
number of genetic networks.
Using a gene therapy technique,
Yamanaka introduced additional copies of each of the four factors into
mature skin cells using viral vectors—
tiny synthetic viruses that shuttled the
genes right into the chromosomes.
(See illustration at right.)
Yamanaka found that the combined activation of the four factors
caused the skin cells to de-evolve back
into cells that bore a striking similarity to embryonic stem cells.
The genome of a skin cell can be manipulated to
reverse its developmental clock, resulting in a cell
identical to an embryonic stem cell.
Four genes, Oct4, Sox2, c-Myc, and Klf4, are
encapsulated into separate viral vectors and
inserted into the nucleus of a skin cell.
Each of these four genes lands
randomly on a chromosome.
CHRISTINA ULLMAN
Rethinking reprogramming
For years, creating embryonic stem
cells without embryos like this had
been a major goal for Jaenisch. He
had concluded that using human
embryos to generate embryonic stem
cells for actual medical use would
never be practical, both for technical
reasons and because of societal concerns about such cells.
He was astonished by the prospect of accomplishing this with a mere
four genes. So were Hochedlinger
and their peers in the inner circle of
embryonic stem cell research.
But Yamanaka’s accomplishment
also drew considerable skepticism and
relatively little interest from the outside world. One big reason was what
had made 2006 the worst of years—
the final collapse of Korean scientist Hwang Woo-Suk’s claim to have
created human embryonic stem cells
through nuclear transfer.
Yamanaka’s work was solid science, but “to be perfectly honest,
many of us didn’t even believe it,”
admits Hochedlinger. “Four transcription factors reprogramming a cell? It
just seemed too simple.”
Additionally, the new cells were
limited when compared with naturally derived embryonic stem cells,
mainly in that they couldn’t produce
live chimeric mice. And Yamanaka
was unable to generate live mice—the
definitive experiment for demonstrating that a stem cell is embryonic.
Even after Yamanaka published a
paper in Cell in August 2006 describing exactly how he had done the
Each new gene integrates into the genome,
and starts acting like a normal gene.
These four genes end up affecting the entire genome
of the skin cell to such an extent that its developmental
clock is reversed. Soon, the skin cell is transformed and
becomes virtually identical to an embryonic stem cell.
reprogramming, most reseachers sat
on their hands.
But as Yamanaka’s lab charged
forward, two other groups eagerly
plunged ahead to reproduce—and
improve—the technique.
One group was led by Hochedlinger and Kathrin Plath from the
Institute for Stem Cell Biology and
Medicine at the University of California/Los Angeles, and another by
Jaenisch’s Whitehead lab. That group
included postdoctoral researchers
Marius Wernig, Alexander Meissner
and Tobias Brambrink; graduate student Ruth Foreman; and Manching
Ku, a research fellow from Bradley
Bernstein’s lab at MGH.
And this June, all three labs pub-
lished papers confirming and extending Yamanaka’s work.
Although all the experiments
occurred in mice and have yet to be
demonstrated in human cells, the field
of embryonic stem cell research got a
major jolt of energy—and headlines
around the world.
Irving Weissman, one of the
world’s leading stem cell scientists,
declared to the New York Times that
“this is about as big a deal as you
could imagine.”
Success on the big screening
The scientists drew on well-established genetic and biochemical
procedures, as well as almost endless
patience, to create and test the cells.
19
embryonic stem cells
Jaenisch’s group successfully used
the same technique as the Yamanaka
lab to activate Oct4, Sox2, c-Myc and
Klf4 in mouse skin cells. The key difference in its approach was the screening technique used to sort through
these cells.
“We were working with tens of
thousands of cells, and we needed
to devise a precise method for picking out those rare cells in which the
reprogramming actually worked,”
says Wernig. The odds were not in
their favor—only about one in 1,000
cells made the cut.
The group focused on Oct4 and
another transcription factor called
Nanog, two identifying hallmarks
that are active in embryonic stem cells
that are fully pluripotent (able to spin
off cells that differentiate into almost
every cell in the adult body). The trick
was to figure out a way to harvest
Oct4- and Nanog-active cells from the
rest of the population.
The answer came in a common
laboratory technique called “homologous recombination.”
Here, the scientists took genetic
material known to be resistant to the
toxic drug neomycin and spliced it
into the genomes of each cell right
beside Oct4 and Nanog. If Oct4 and
Nanog were switched on, the drugresistant DNA would also spring into
action, conferring immunity. When
they added the drug to the batch,
only the Oct4- and Nanog-active cells
could resist it. Thus, the research-
Identity crises
This summer, scientists in the
lab of Whitehead Member Richard Young surprised themselves
with a discovery that may help
to explain the success of the
embryonic stem cell reprogramming experiments: Many
human genes hover between
“on” and “off” in any given cell.
According to a study published online in Cell in July,
these genes begin making RNA
templates for proteins but fail
20
adding an additional level of proof for
these cells’ pluripotency.
Finally, the team exploited
another lab technique that involves
creating a genetically abnormal
embryo whose cells all consist of four
chromosomes, rather than the usual
two. Such an embryo can only form
a placenta, and cannot develop into a
full-term fetus.
The researchers injected the reprogrammed cells into
Prove it
this embryo, and then
But definitive evidence
implanted it in a uterus.
would come only by
Eventually, viable lateproving that these cells
gestation fetuses could
could develop into any
be recovered—created
kind of cell type or
exclusively from the
body tissue.
reprogrammed cells.
The Jaenisch group
“This is the most strinapproached this quesgent criteria anyone can
tion in three ways.
use to determine if a
Rudolf Jaenisch was surprised
First, they fluocell is pluripotent,” says
by the power four genes brought
rescently labeled the
Jaenisch.
to reprogramming an adult cell
reprogrammed cells
Both Hochedlinger
into an embryonic state.
and injected them into
and Yamanaka also creearly-stage embryos,
ated chimeric mice from
which eventually gave rise to live
such reprogrammed cells and then
mice. While these mice consisted of
bred these mice and created new genboth the reprogrammed cells and
erations. In addition, Hochedlinger
the natural cells from the original
described reactivation of the silent
embryo, the fluorescent tags indicated
X chromosome, which is shut down
that the reprogrammed cells contribin differentiated female cells, adding
uted to all tissue types—everything
another level of pluripotency.
from blood to internal organs to hair
Any one of these papers would
color.
have caused quite a stir. But all three
Next, they bred these mice and
papers were published simultanefound lineages of the reprogrammed
ously—Jaenisch and Yamanaka in
cells in the subsequent generation,
Nature, and Hochedlinger in Cell
ers ensured that only fully reprogrammed, pluripotent embryonic stem
cells survived.
The team ran these cells through
a battery of tests, searching for any
substantial differences from normal
embryonic stem cells. Their genetic
markers were identical. So were the
markers for epigenetic effects (which
differentiate cells without changing
the underlying genes).
to finish. The templates never
materialize, and the proteins
never appear.
“Surprisingly, about onethird of our genes, including all
the regulators of cell identity,
fall into this new class,” says
Young. “It seems awfully risky
for an adult cell to leave genes
primed that could change its
identity.”
“These genes are like
cars revving their engines
before the beginning of a
race,” explains postdoctoral
researcher Matthew Guenther,
a lead author on the paper.
“They’re not parked in a garage
with their engines off. They’re
at the starting gate, waiting for
a flag that says ‘go.’”
The overzealous “cars”
include all the master regulator
genes responsible for directing
cells along particular developmental paths. Activating such
genes might cause a cell to
assume new properties. And
it could explain why researchers—including those in the lab
of Rudolf Jaenisch, who is an
author on the latest study—
could convert mouse adult skin
cells to embryonic stem cells
by simply introducing four key
genes. Given the right signals,
inactive developmental regulators primed for transcription
could roar to life.
“This could bring us a step
closer to reprogramming cells
in a controlled fashion, which
has important applications for
regenerative medicine,” suggests Young. – Alyssa Kneller
Stem Cell—and that ensured that the
results could not be ignored.
“All three papers validated each
other,” says Jaenisch. “This drove
home the point that reprogramming
without eggs is a biological fact.”
It’s all about the science
Jaenisch cautions that the experiments
are only a starting point, with no
guarantee that the techniques will be
effective with humans. “The questions
that we’ve asked in this study are fundamental questions in developmental
biology,” he says. “From the scientific
perspective, they stand on their own.”
He emphasizes that research on
conventionally derived human embryonic stem cells needs to continue.
“We don’t know about the future, but
for now at least, it’s ‘both/and,’ not
‘either/or,’” agrees Hochedlinger.
Such caveats, however, immediately were buried in an onslaught of
political and media reaction.
Most visibly, two weeks after the
papers appeared, when President Bush
announced he would veto legislation that promised to lift many barriers on stem cell research, he stated
in a White House press release that
“researchers are now developing
promising new techniques that offer
the potential to produce pluripotent
stem cells, without having to destroy
human life—for example, by reprogramming adult cells to make them
function like stem cells.”
Jaenisch is no stranger to seeing others misinterpret his work for
political gain. In the fall of 2005, he
co-published a paper with Meissner
demonstrating how embryonic stem
cells could be culled from a nonviable
embryo-like entity.
Opponents of embryonic stem cell
research seized on this as proof that
there is no need to further explore
nuclear transfer in human cells or to
derive stem cells from embryos discarded by fertility clinics—implications that the paper never suggested.
Honing for humans
Nevertheless, the research has continued moving forward in a way that
brings it one step closer to possible
Researchers in the Jaenisch lab were among those showing that naturally derived embryonic
stem cells from mice (top) are morphologically identical to reprogrammed skin cells (bottom).
medical applications.
In a paper published in Nature
Biotechnology this summer, Wernig
and Meissner report a way to simplify
their earlier experiment. Previously,
they had been forced to genetically
manipulate the original donor cells
to later select for those that had been
thoroughly reprogrammed.
This was problematic for two reasons. First, genetically manipulated
cells would never be approved for
therapies, and second, even if they
were, the techniques used to manipulate them have never been successfully
applied to human cells.
In the new experiment, however,
they isolated reprogrammed cells
from non-reprogrammed cells solely
by examining the cells’ physical attributes. They noticed, for example, that
while the non-reprogrammed cells
are large and flat, the embryonic cells
are small and round and tend to form
tight colonies.
“We still have some challenges,”
cautions Wernig. “The mouse cells
were originally reprogrammed with
retroviruses. That’s something we’d
never do in humans. Still, it’s nice to
know that we can now, theoretically
at least, overcome one hurdle.”
What lies ahead in embryonic stem
cell research and therapies is still an
entirely open question. “But from this
day forward, the world of stem cell
research can’t stay the same,” says
Jaenisch.
21
State of
research
IF MASSACHUSETTS
PUTS BIG BUCKS
INTO BIOMEDICAL
RESEARCH, WHERE
SHOULD THE
MONEY GO?
By Eric S. Brown
illustration by james yang
Massachusetts life scientists may have
different ideas about how to spend the
$1 billion of Governor Deval Patrick’s
proposed Life Sciences Initiative, but
most seem to agree on two points:
Scientific merit and funding need
should drive the selection process.
Stem-cell research should be given
priority.
Filling gaps or taking new paths?
he legislature will set guidelines,
but making the tough decisions on
funding specific research ultimately
will be the job of an expanded Massachusetts Life Science Center committee. The committee will face
T
22
scrutiny and pressure from anti-stemcell-research activists, anti-tax crusaders and a host of pleading research
hospitals and academic institutions.
To avoid conflicts of interest in
doling out research grants, scientists
call for a merit-based formula. “I
strongly support a peer-review process with study sections much like
those of the National Institutes of
Health,” says MIT Institute Professor
Robert Langer, who won this year’s
National Medal of Science for his
cancer drug delivery research.
The governor has stated that
some grants would support proposals that receive high NIH scores but
don’t receive funding. “Bridging NIH
gap funding is really important, and
it helps to avoid politics because
the applications are already peerreviewed,” says Joan Brugge, chair of
Harvard Medical School’s department
of cell biology. “A lot of us have been
denied grants that received superb
scores, so we spend half our time
“The first business of the state is to maintain
an educated work-pool. If those needs are met,
other things will follow.” – PHILLIP SHARP
looking for resources.”
Phillip Sharp, MIT Institute Professor and Nobel laureate, agrees
with the governor’s plan to focus
funding on shared projects that could
be widely beneficial. “It should be
focused,” he says. “If you spread it
too far it won’t have an impact.”
Yet Sharp says it’s also important
to support cutting-edge research. “I’d
rather see it invested in new initiatives rather than fill gaps in funding,”
he says, mentioning neurobiology and
biofuels as two promising areas.
For her part, Brugge recommends
systems biology, tissue modeling and
engineering-based research.
Centralizing innovation
he initiative also calls for setting up “innovation centers” to
streamline technology transfer and
funding. Once again, biologists may
differ on this approach.
Brugge likes the idea. “There’s a
need for core services that encourage
collaboration,” she says.
Yet Tariq Rana, director of chemical biology at the University of Massachusetts Memorial Medical School
in Worcester, worries that such a
focus could ignore cash-starved innovators. “Let scientific needs guide
these collaborations rather than forcing people to collaborate,” Rana
says. “Innovations come from investigator-initiated ideas.”
T
Banking on stem cells
s it currently stands, the initiative would use bonds to build
the nation’s first centralized human
embryonic stem cell (hESC) repository. This facility would store and
share hESC lines developed by Massachusetts scientists.
A major question facing the legislature is whether such stem-cell
projects should be given priority for
biomedical research funds.
Like most of the scientists con-
A
tacted for this story, Whitehead
Member Robert Weinberg thinks so.
“We should invest in projects that
are impossible without this money
and that have the greatest multiplier
effect,” he says. “Stem cells hold
enormous promise for all kinds of
biomedical research.”
But Weinberg is skeptical that an
hESC repository is the best investment: “Historically, such banks
haven’t had much of an impact.”
“State funding for hESC research
would be very important, especially
given the current anemic level of
federal support,” emphasizes Willy
Lensch, a Harvard Medical School
instructor who works with hESC
lines at Children’s Hospital in Boston.
Critical mass at UMass
he governor’s first two bond recommendations—the hESC repository and an RNAi Therapeutics
Center that’s already under way—are
both UMass Medical projects.
Patrick also proposed upgrading
life sciences research and educational
facilities throughout the UMass system and providing it with workforce
training funds.
Scientists generally support the
UMass educational investments. “It’s
T
appropriate to spend taxpayer money
at the state university,” says Sharp.
“The first business of the state is to
maintain an educated work-pool. If
those needs are met, other things will
follow.”
“It’s about time to invest in public
life-sciences education,” says Rana,
who formed Worcester-based RXi
Pharmaceuticals with 2006 Nobel
laureate Craig Mello and Michael
Czech, another UMass scientist. “It’s
essential to serve students and communities of all economic and social
backgrounds.”
“It’s people who make the biggest difference,” says Weinberg. “We
need state-supported training programs at the bachelor’s level. These
are the people who actually get the
work done.”
But he questions whether the state
is reinventing the wheel in advanced
research. “The money shouldn’t all
go to rich institutions, but UMass
may not be prepared to profitably
infuse the funds,” he says.
Better living through biology
hile they agree on the need for
the state to remain competitive,
researchers also emphasize the huge
potential for biomedical research to
save and improve lives.
“It’s good that the state is providing funds for life sciences,” says
Langer. “It’s not just about the economy. It’s about our children’s health
and our own.”
W
How (and why) to bet a billion
Massachusetts Governor
Deval Patrick’s Life Sciences
Initiative plan calls for $500
million in bonds for facilities and equipment, $250
million for tax benefits and
incentives, and $250 million
for research grants, fellowships and training. Another
$250 million in matching
private-sector grants could
boost the total to $1.25 billion over 10 years.
Patrick’s billion-dollar
gamble reflects the state
biotech arms race kicked
off by California’s $3 billion
stem cell research program.
Other states are joining
in enthusiastically—New
York has launched a $1 billion stem cell effort, for
instance, and Texas voters
are eyeing a referendum on
a $3 billion cancer research
initiative in a November
state election.
The Commonwealth,
which hosts one in seven
U.S. biotechnology workers,
may have the most to lose
in the race. “Massachusetts
has a large cadre of biologists who are international
leaders, but they will be
lured away if we cannot
come up with good packages,” says Whitehead’s
Robert Weinberg. “Other
states will invest a lot to
attract our talent.”
23
UNSUNG
HEROINES
( )
WHILE YOUNG
RESEARCHERS
COME AND GO,
CAREER TECHNICIANS
KEEP THE LABS
HUMMING
“When you start a lab, it is just you and group of people—some of whom have been
the lab technician,” says Whitehead Member
working in the labs almost as long as the
David Bartel.
senior scientists who hired them.
“In our case, the techs did some of the fun“Whitehead has the biggest collection of
damental early work,” Bartel adds. “They’re
senior technicians I have ever seen,” remarks
often the most flexible when it comes to fillPaula Grisafi, lab manager for Whitehead
ing some really important gap. As our lab has Member Gerald Fink. “The researchers really
gotten bigger, they have turned to filling the
need the continuity and experience of technineed we have now, which is moving existing
cians who have been doing it a long time.”
projects faster.”
Here are three of the veterans who have
All throughout Whitehead,
been working behind the
scientific advances depend on
scenes for two decades or
By Carol Cruzan Morton
the daily tasks of this hidden
even more.
photographs by john soares
24
FROM DAY ONE
AT WHITEHEAD
After 31 years in the lab of
Whitehead Member Harvey
Lodish, Naomi Cohen is well past
retirement age. But she’s still sharing lab manager duties with Claire
Katidas. “If you hang around long
enough, you end up doing lab
management,” she says.
Cohen graduated in zoology
from Barnard College in the early
’40s and worked as a technician
while she contemplated graduate
school. But the prospect of running a lab filled her with trepidation. “When I met my husband,
I bagged the whole thing,” she
recalls. “I wanted a family life and
a well-rounded personal life, and
I didn’t believe I could do both.”
Three children and 14 years later,
Cohen eagerly returned to the lab.
Her work nurturing slime
molds for early genetic studies, among other duties, went
smoothly for the first nine years.
Then the Lodish group moved
into the first labs in the new
Whitehead building in the summer of 1984. No amount of tinkering could make the molds grow.
Cohen was distressed, and the
woman who mixed the growing
media was in tears every day.
The problem was pinpointed
by visiting professor Bill Loomis,
the “godfather of slime molds,”
Cohen says. “His father before
him was involved in slime molds
and told him, ‘The first thing you
do when you set up the lab is to
set up the still.’” The Lodish lab’s
old MIT building had stills on the
roof. The new building’s water
purification system rendered the
water too pure for slime molds.
Cohen revived the lab’s dormant slime mold stocks for her
first original research paper at
age 61. “I was the last person to
work with them,” she says. “We
still have them frozen away.”
“IF YOU HANG AROUND LONG
ENOUGH, YOU END UP DOING
LAB MANAGEMENT.”
Naomi Cohen
published her
first original research
paper at 61.
– N AOMI CO HEN
25
unsung heroines
THRIVING ON
THE BENCH
To young scientists these days,
sequencing DNA may not seem
like rocket science.
But three decades ago, when
lab technician Paula Grisafi was
preparing DNA for analysis in
the lab of MIT biology professor
David Botstein, she actually used
rocket fuel in one step in the
labor-intensive process.
“The two things I really provide are continuity and lab memory,” says Grisafi, now in her 19th
year in the Gerald Fink lab.
Like many young technicians,
Grisafi once intended to go to
graduate school. Then her dad
died. The oldest of seven siblings, she moved back to Long
Island to help her family and
took a lab job at nearby Cold
Spring Harbor Laboratory. She
has thrived on the job ever since.
“By the time I hit 30, I realized I really love bench science,”
Grisafi says. “I realized that principal investigators don’t get to
do what I really like to do. They
have to write grants, serve on
committees and travel to meetings. I get to do all the good
stuff.”
Grisafi also likes leaving her
work at the lab and spending
nights and weekends on outside
interests, which include scriptwriting. In 2005, the American
Film Institute hosted a workshop
for Grisafi and 14 other scientists. She is on her third movie
script, this one about a high
school teacher who accidentally discovers a way to generate
increased power from photosynthesis. She’s also turning one of
her stories into a book.
“PRINCIPAL INVESTIGATORS
DON’T GET TO DO WHAT I REALLY
LIKE TO DO.”
Paula Grisafi
writes movie
scripts on the
side.
– PAUL A GRISA FI
26
“I WOULD LEAVE [DAVID PAGE] A LIST
OF THINGS HE NEEDED TO DO, AND
THEN HE’D LEAVE ME A NOTE TO
PICK UP FROM IN THE MORNING.”
– L AUR A BROWN
Laura Brown
arrives early
each morning in David
Page’s lab.
AROUND
THE CLOCK
Laura Brown has been working
for Whitehead Director David
Page since 1984, when he was a
Whitehead Fellow and she had
just graduated in biochemistry
from Trinity College in Hartford.
Between her early-bird schedule and his late nights, they kept
experiments going around the
clock. “I would leave a list of
things he needed to do, and then
he’d leave me a note to pick up
from in the morning,” she says.
One of the most rewarding moments in her career came
when she aided Page and his collaborators in sequencing the Y
chromosome. She helped fill in
gaps and contributed to the figures published in the 2003 paper.
Brown was less satisfied
with her role as the enforcer of
an ever-growing list of scientific
regulations. One low point came
when a stench rose from vats of
e. coli bacteria in an unauthorized experiment a graduate student had set up in the communal
warm room.
She still arrives by daybreak
from her home in Cape Cod on a
4:20 a.m. bus to Boston packed
with beach-loving commuters.
Now bumped up from technician to lab manager, she helps
Page with lectures and outside
presentations. Last year, she
spent most of her time meeting with contractors and electricians to help move the lab to a
new space. (Sadly, the years of
accumulated spermatozoa jokes
taped around the old lab were
lost in the shuffle.)
Brown’s duties may have
changed, but her purpose
remains the same. “I’m in it for
the good of the lab,” she says.
And by 4 p.m., she is home
with time to enjoy the beach and
her garden.
27
Whitehead tales
28
|
story: Carol Cruzan Morton illustrations: Peaco Todd
29
Neutrophils, shown here in pink, are
white blood cells that cruise around
the body identifying and destroying
invaders. The discovery that these
cells recognize and respond to a
particular form of sugar contained
on the surface of pathogenic fungi
may lead to more effective antifungal drugs. For details, see page 4.
Whitehead Institute for Biomedical Research
Nine Cambridge Center
Cambridge, Massachusetts 02142-1479
Non-Profit Org.
US Postage
PAID
Cambridge, MA
Permit No. 56998

Fall 2007 PDF - Whitehead Institute for Biomedical Research

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