David Kirkpatrick

July 3, 2009

Stem cell news — differences and ethics

Two releases from yesterday on stem cells. Number one is on the found differences between reprogrammed skin cells and embryonic stem cells. Second is a call for stem cell debates by bioethicists before the science gets too far ahead of ethical considerations.

The first release:

UCLA scientists find molecular differences between embryonic stem cells and reprogrammed skin cells

UCLA researchers have found that embryonic stem cells and skin cells reprogrammed into embryonic-like cells have inherent molecular differences, demonstrating for the first time that the two cell types are clearly distinguishable from one another.

The data from the study suggest that embryonic stem cells and the reprogrammed cells, known as induced pluripotent stem (iPS) cells, have overlapping but still distinct gene expression signatures. The differing signatures were evident regardless of where the cell lines were generated, the methods by which they were derived or the species from which they were isolated, said Bill Lowry, a researcher with the Broad Stem Cell Research Center and a study author.

“We need to keep in mind that iPS cells are not perfectly similar to embryonic stem cells,” said Lowry, an assistant professor of molecular, cell and developmental biology. “We’re not sure what this means with regard to the biology of pluripotent stem cells. At this point our analyses comprise just an observation. It could be biologically irrelevant, or it could be manifested as an advantage or a disadvantage.”

The study appears in the July 2, 2009 issue of the journal Cell Stem Cell.

The iPS cells, like embryonic stem cells, have the potential to become all of the tissues in the body. However, iPS cells don’t require the destruction of an embryo.

The study was a collaboration between the labs of Lowry and UCLA researcher Kathrin Plath, who were among the first scientists and the first in California to reprogram human skin cells into iPS cells. The researchers performed microarray gene expression profiles on embryonic stem cells and iPS cells to measure the expression of thousands of genes at once, creating a global picture of cellular function.

Lowry and Plath noted that, when the molecular signatures were compared, it was clear that certain genes were expressed differently in embryonic stem cells than they were in iPS cells. They then compared their data to that stored on a National Institutes of Health data base, submitted by laboratories worldwide. They analyzed that data to see if the genetic profiling conducted in other labs validated their findings, and again they found overlapping but distinct differences in gene expression, Lowry said.

“This suggested to us that there could be something biologically relevant causing the distinct differences to arise in multiple labs in different experiments,” Lowry said. “That answered our first question: Would the same observation be made with cell lines created and maintained in other laboratories?”

Next, UCLA researchers wanted to confirm their findings in iPS cell lines created using the latest derivation methods. The cells from the UCLA labs were derived using an older method that used integrative viruses to insert four genes into the genome of the skin cells, including some genes known to cause cancer. They analyzed cell lines derived with newer methods that do not require integration of the reprogramming factors. Their analysis again showed different molecular signatures between iPS cells and their embryo-derived counterparts, and these signatures showed a significant degree of overlap with those generated with integrative methods.

To determine if this was a phenomenon limited to human embryonic stem cells, Lowry and Plath analyzed mouse embryonic stem cells and iPS lines derived from mouse skin cells and again validated their findings. They also analyzed iPS cell lines made from mouse blood cells with the same result

“We can’t explain this, but it appears something is different about iPS cells and embryonic stem cells,” Lowry said. “And the differences are there, no matter whose lab the cells come from, whether they’re human or mouse cells or the method used to derive the iPS cells. Perhaps most importantly, many of these differences are shared amongst lines made in various ways.”

Going forward, UCLA researchers will conduct more sophisticated analyses on the genes being expressed differently in the two cell types and try to understand what is causing that differential expression. They also plan to differentiate the iPS cells into various lineages to determine if the molecular signature is carried through to the mature cells. In their current study, Lowry and Plath did not look at differentiated cells, only the iPS and embryonic stem cells themselves.

Further study is crucial, said Mark Chin, a postdoctoral fellow and first author of the study.

“It will be important to further examine these cells lines in a careful and systematic manner, as has been done with other stem cell lines, if we are to understand the role they can play in clinical therapies and what effect the observed differences have on these cells,” he said.

 

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The stem cell center was launched in 2005 with a UCLA commitment of $20 million over five years. A $20 million gift from the Eli and Edythe Broad Foundation in 2007 resulted in the renaming of the center. With more than 150 members, the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research is committed to a multi-disciplinary, integrated collaboration of scientific, academic and medical disciplines for the purpose of understanding adult and human embryonic stem cells. The center supports innovation, excellence and the highest ethical standards focused on stem cell research with the intent of facilitating basic scientific inquiry directed towards future clinical applications to treat disease. The center is a collaboration of the David Geffen School of Medicine, UCLA’s Jonsson Cancer Center, the Henry Samueli School of Engineering and Applied Science and the UCLA College of Letters and Science. To learn more about the center, visit our web site at http://www.stemcell.ucla.edu.

Head below the fold for the second release on a call for an ethics debate on stem cells. (more…)

December 15, 2008

Converting to stem cells

Well, stem cell-like cells.

The release:

Single virus used to convert adult cells to embryonic stem cell-like cells

CAMBRIDGE, Mass. (Dec. 15, 2008) — Whitehead Institute researchers have greatly simplified the creation of so-called induced pluripotent stem (iPS) cells, cutting the number of viruses used in the reprogramming process from four to one. Scientists hope that these embryonic stem-cell-like cells could eventually be used to treat such ailments as Parkinson’s disease and diabetes.

The earliest reprogramming efforts relied on four separate viruses to transfer genes into the cells’ DNA–one virus for each reprogramming gene (Oct4, Sox2, c-Myc and Klf4). Once activated, these genes convert the cells from their adult, differentiated status to an embryonic-like state.

However, this method poses significant risks for potential use in humans. The viruses used in reprogramming are associated with cancer because they may insert DNA anywhere in a cell’s genome, thereby potentially triggering the expression of cancer-causing genes, or oncogenes. For iPS cells to be employed to treat human diseases, researchers must find safe alternatives to reprogramming with such viruses. This latest technique represents a significant advance in the quest to eliminate the potentially harmful viruses.

Bryce Carey, an MIT graduate student working in the lab of Whitehead Member Rudolf Jaenisch, spearheaded the effort by joining in tandem the four reprogramming genes through the use of bits of DNA that code for polymers known as 2A peptides. Working with others in the lab, he then manufactured a so-called polycistronic virus capable of expressing all four reprogramming genes once it is inserted into the genomes of mature mouse and human cells.

When the cells’ protein-creating machinery reads the tandem genes’ DNA, it begins making a protein. However, when it tries to read the 2A peptide DNA that resides between the genes, the machinery momentarily stops, allowing the first gene’s protein to be released. The machinery then moves on to the second gene, creates that gene’s protein, stalls when reaching another piece of 2A peptide DNA, and releases the second gene’s protein. The process continues until the machinery has made the proteins for all four genes.

Using the tandem genes, Carey created iPS cells containing just a single copy of the polycistronic vector instead of multiple integrations of the viruses. This significant advancement indicates that the approach can become even safer if combined with technologies such as gene targeting, which allows a single transgene to be inserted at defined locations.

Interestingly, while Carey’s single-virus method integrates all four genes into the same location, it has proven to be roughly 100 times less efficient than older approaches to reprogramming. This phenomenon remains under investigation.

“We were surprised by the lower efficiency,” Carey says. “We’re not sure why, but we need to look what’s going on with expression levels of the polycistronic virus’s proteins compared to separate viruses’ proteins.”

Although the one virus method is less efficient, Jaenisch maintains it represents an important advance in the field.

“This is an extremely useful tool for studying the mechanisms of reprogramming,” says Jaenisch, who is also a professor of biology at MIT. “Using this one virus creates a single integration in the cells’ DNA, which makes things much easier to handle.”

 

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Written by Nicole Giese

Rudolf Jaenisch’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a professor of biology at Massachusetts Institute of Technology.

Full citation:

PNAS, online between December 15 and December 19

“Reprogramming of murine and human somatic cells using a single polycistronic vector”

Bryce W. Carey (1,2), Styliani Markoulaki (1), Jacob Hanna (1), Kris Saha (1), Qing Gao (1), Maisam Mitalipova (1), and Rudolf Jaenisch (1,2)

1. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.

2. Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.

September 26, 2008

Stem cells from adult cells

I’m for stem cell research of all stripes, but it is encouraging that research is ongoing beyond just embryonic stem cells such as this application using adult cells.

This is good medical news. But no reason to not lift the asinine theocratic ban on US government support of embryonic stem cell research.

From the link:

Last year, researchers announcedone of the most promising methods yet for creating ethically neutral stem cells: reprogramming adult human cells to act like embryonic stem cells. This involved using four transcription factor proteins to turn specific genes on and off. But the resulting cells, called induced pluripotent stem (iPS) cells for their ability to develop into just about any tissue, have one huge flaw. They’re made with a virus that embeds itself into the cells’ DNA and, over time, can induce cancer. Now, scientists at Harvard University have found a way to effect the same reprogramming without using a harmful virus–a method that paves the way for tissue transplants made from a patient’s own cells.

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