Stem cells made by reprogramming adult cells remember tissue of
26 July 2010
Adult cells that have been reprogrammed into induced
pluripotent stem cells (iPS cells) keep a memory of their tissue of
origin, according to researchers at Children's Hospital Boston,
John Hopkins University and their colleagues. This could limit their
ability to function as a less controversial alternative to embryonic
stem cells for basic research and cell replacement therapies.
The findings, published in Nature, highlight a major
challenge in developing clinical and scientific applications for the
powerful new technique of making iPS cells, which, like embryonic
stem cells, have the capacity to differentiate into any type of cell
in the body. Similar findings were published simultaneously online
in Nature Biotechnology by other Boston researchers.
"iPS cells retain a 'memory' of their tissue of origin," said
senior author George Daley, MD, PhD, a Howard Hughes Medical
Institute investigator and Director of the Stem Cell Transplantation
Program at Children's. "iPS cells made from blood are easier to turn
back into blood than, say, iPS cells made from skin cells or brain
In contrast, another technique known as nuclear transfer creates
pluripotent stem cells without apparent memory and equally adept at
transforming into several tissue types, the paper reports. In iPS
cells, the memory of the original donor tissue can be more fully
erased with additional steps or drugs, the researchers found, which
made those iPS cells as good as the nuclear-transfer stem cells at
generating different types of early tissue cells in lab dishes.
The residual cellular memory comes in part from lingering
genome-wide epigenetic modifications to the DNA that gives each cell
a distinctive identity, such as skin or blood, despite otherwise
identical genomes. In the study, the persistent bits of a certain
type of epigenetic modification called methylation were so
distinctive in iPS cells that their tissues of origin could be
identified by their methylation signatures alone.
"We found the iPS cells were not as completely reprogrammed as
the nuclear transfer stem cells," said co-senior author Andrew
Feinberg, MD, MPH, director of the Center for Epigenetics at Johns
Hopkins, whose group did systematic epigenomic analyses of the
cells. "Namely, DNA methylation was incompletely reset in iPS cells
compared to nuclear transfer stem cells. Further, the residual
epigenetic marks in the iPS cells helped to explain the lineage
restriction, by leaving an epigenetic memory of the tissue of origin
Epigenetic memory may be helpful for some applications, such as
generating blood cells from iPS cells originally derived from a
person's own blood, the researchers said. But the memory may
interfere with efforts to engineer other tissues for treatment in
diseases such as Parkinson's or diabetes or to use the cells to
study the same disease processes in laboratory dishes and test drugs
for potential treatments and toxicities.
"These findings cut across all clinical applications people are
pursuing and whatever disease they are modeling," said Daley, also a
member of the Harvard Stem Cell Institute and professor of
biological chemistry and molecular pharmacology at Harvard Medical
School. "Our data provide a deeper understanding of the iPS
platform. Everyone working with these cells has to think about the
tissues of origin and how that affects reprogramming."
iPS cells became a focal point of stem cell biology four years
ago when a Japanese team led by Shinya Yamanaka created the
functional equivalent of embryonic stem cells from adult mouse skin
cells with a cocktail of four molecular factors. A year later,
Yamanaka's team, Daley's team and a University of Wisconsin group
all independently reported creating human iPS cells from adult skin
cells, raising hopes for future clinical and research applications.
Earlier this month, Daley's team and two other groups reported
making human iPS cells from adult blood cells, a faster and easier
source. In that study, iPS cells from blood were also better at
differentiating back into blood cells than into other tissue types.
In the current study, first author Kitai Kim, PhD, postdoctoral
fellow in the Daley lab, tested mice iPS cells head-to-head with
pluripotent cells made through somatic cell nuclear transfer. Best
known as the cloning method that created the sheep Dolly fourteen
years ago, nuclear transfer reprograms an adult cell by transferring
its nucleus into an unfertilized egg cell, or oocyte, whose nucleus
has been removed. The process of transferring the nucleus
immediately reprograms it epigenetically, replicating the same
process that happens to sperm upon fertilization, Kim said.
"Stem cells generated by somatic cell nuclear transfer are on
average, closer to bona fide embryonic stem cells than are iPS
cells," Daley said. "This has an important political message -- we
still need to study the mechanisms by which nuclear transfer
reprograms cells, because the process seems to work more efficiently
and faithfully. Learning the secrets of nuclear transfer may help us
make better iPS cells."
Kim began the study with older mice (ages 1 to 2), aiming to
emulate the future human clinical scenario, which is likely to
involve older people. Older cells are set in their ways and harder
to reprogram, Kim said. Kim originally wanted to compare the
transplantation success of blood cells made from three different
pluripotent sources: iPS cells, embryonic stem cells (the gold
standard), and nuclear transfer stem cells.
He did not get as far as transplantation. "Even in vitro we
observed strikingly different blood-forming potential," he and his
co-authors wrote in the paper. "We focused instead on understanding
iPS cells from blood were best at making blood, and fibroblasts
were best at differentiating into bone, a closely related tissue,
Kim and his colleagues found. The researchers could reset the iPS
cells more fully by differentiating them first into blood cells and
then reprogramming them again, or by treating them with drugs that
change their epigenetic profile.
In contrast, nuclear transfer stem cells from the same sources --
blood cells and skin - were equally able to differentiate into blood
and bone, Kim and his colleagues found. Like iPS cells, the nuclear
transfer technique also creates patient-specific cells, but has not
yet proven successful with human cells.
"This paper opens our eyes to the restricted lineage of iPS
cells," said Feinberg. "The lineage restriction by tissue of origin
is both a blessing and a curse. You might want lineage restriction
in some cases, but you may also have to do more work to make the iPS
cells more totally pluripotent."
Another study published online simultaneously in the journal
Nature Biotechnology reports similar findings. "Our
paper comes to a similar conclusion that a retention of memory
reflects the cell of origin and affects the capacity of the iPS cell
to differentiate into other cell types," said senior author Konrad
Hochedlinger, PhD, a stem cell biologist at the Massachusetts
General Hospital Center for Regenerative Medicine and, like Daley, a
member of the Harvard Stem Cell Institute, who demonstrated another
method to more fully reprogram iPS cells. "When we let the cells go
through a lot of cell divisions, they lose the memory," he said.