Scientists Home in on Chemicals Needed to Reprogram Cells

Groundbreaking discovery moves field closer to therapeutic applications
Friday, 03 December 2010

Scripps Research Institute scientists have made a significant leap forward in the drive to find a way to safely reprogram mature human cells and turn them into stem cells, which can then change into other cell types, such as nerve, heart, and liver cells. The ability to transform fully mature adult cells such as skin cells into stem cells has potentially profound implications for treating many diseases.

Scripps Research Associate Professor

Sheng Ding.

In research published in the December 3, 2010 issue of Cell Stem Cell, Scripps Research Associate Professor Sheng Ding, PhD, reports a novel cocktail of drug-like small molecules that, with the assistance of a gene called Oct4, enables reprogramming of human skin cells into stem cells.

"Our ultimate goal is to generate induced pluripotent stem cells with defined small molecules," Ding said.

"This would offer a fundamentally new method and significant advantages over previous methods, such as genetic manipulation or more difficult-to-manufacture biologics."

Using small-molecule compounds to reprogram adult human cells back to their pluripotent state — able to change into all other cell types — avoid the ethical controversy around embryonic stem cell research, and pave the way for the large-scale production of stem cells that could be used inexpensively and consistently in drug development. Cures for Alzheimer's, Parkinson's, and many other diseases might be possible if new cells could be created from a patient's own cells to replace those that have succumbed to disease or injury.

Substituting Chemicals for Genes
Scientists discovered in 2007 that fully differentiated mature cells, such as skin cells, could be "reprogrammed" to become pluripotent by using four transcription genes. One problem with this technique is that these genes, once inserted into a cell, permanently alter the host cell's DNA.

"There are many concerns when the host cell's genome is manipulated," Ding says.

"One major worry is that since the four genes are [cancer-causing] oncogenes, they could induce tumours or interrupt functions of other normal genes."

Because of this danger, scientists have been searching for methods that could induce reprogramming without the use of these cancer-causing genes. The method the Ding lab has been pioneering — using small, synthetic molecules — represents a fundamentally different approach from the previous methods.

"We are working toward creating drugs that are totally chemically defined, where we know every single component and precisely what it does, without causing genetic damage," Ding says.

Breaking New Ground
Scientists have known for at least 50 years that a cell's identity is reversible if given the right signal — cells go forward to become mature, functional cells or they can go backward to become primitive cells. In order for cellular reprogramming to be safe and practical enough to use in cell therapy, researchers have sought an efficient, reliable way to trigger the reprogramming process.

In 2008, the Ding lab reported finding small molecules that could replace two of the required four genes. Now, two years later, through extraordinary effort and unique screening strategy, the lab made a major leap forward by finding a way to replace three out of the four genes.

"We are only one step away from the ultimate goal, which would represent a revolutionary technology," Ding says.

The new study also revealed that the novel compound facilitates a novel mechanism in reprogramming: the metabolic switch from mitochondrial respiration to glycolysis, an important mechanism for tissue regeneration. The small molecules Ding and his colleagues found promote reprogramming by facilitating such metabolic switching — an entirely new understanding of reprogramming.

A future goal is to replace Oct4, a master regulator of pluripotency, in the chemical cocktail.

"That would be the last step toward achieving the Holy Grail," Ding says.

"Our latest discovery brings us one step closer to this dream."

Source: Scripps Research Institute
Contact: Mika Ono

Reference:
Reprogramming of Human Primary Somatic Cells by OCT4 and Chemical Compounds
Saiyong Zhu, Wenlin Li, Hongyan Zhou, Wanguo Wei, Rajesh Ambasudhan, Tongxiang Lin, Janghwan Kim, Kang Zhang, Sheng Ding
Cell Stem Cell, Volume 7, Issue 6, 651-655, 3 December 2010, doi:10.1016/j.stem.2010.11.015
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ZenMaster

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Bone Marrow Stromal Stem Cells May Aid in Stroke Recovery

Bone Marrow Stromal Stem Cells May Aid in Stroke Recovery
Thursday, 02 December 2010

A research study from the Farber Institute for Neurosciences and the Department of Neuroscience at Thomas Jefferson University determines bone marrow stromal stem cells may aid in stroke recovery. The results is published in Cell Transplantation – The Regenerative Medicine Journal, issue 19(9).

The study examining the effects of a systematic administration of either rat (allogenic) or human (xenogenic) bone marrow stem cells (MSC) administered to laboratory rats one day after their simulated strokes found "significant recovery" of motor behaviour on the first day. Early administration was found to be more effective than administration seven days after the simulated strokes.

"The timing of stem cell treatment was critical to the magnitude of the positive effects," said the study's lead author, Lorraine Iacovitti, Ph.D., professor, Department of Neuroscience at Jefferson Medical College of Thomas Jefferson University.

"In the host animals we found profound changes and preserved brain structure along with long-lasting motor function improvement."

According to Dr. Iacovitti, there has been little research into just how stem cell transplantation modifies inflammatory and immune effects as well as promotes regenerative effects, such as blood vessel growth. They observed increased activation of microglia as well as modification of the circulating levels of cytokines and growth factors, including elevated VEGF and new blood vessel formation (angiogenesis) following transplantation.

"The mechanism through which MSCs achieve these remarkable effects remains elusive," said Dr. Iacovitti.

"It is possible that activated glia cells (non-neuronal cells that perform a number of tasks in the brain) may play some role in the response, perhaps by partitioning off the infarcted region and limiting the spread of ischemic brain damage without inducing scar formation."

The research team concluded that there was "little doubt" that the administration of stem cells can modify the cellular and molecular landscape of the brain and blood, limiting damage and protecting the stroke-injured brain.

Source: Thomas Jefferson University
Contact: Ed Federico

Reference:
Changes in Host Blood Factors and Brain Glia Accompanying the Functional Recovery after Systemic Administration of Bone Marrow Stem Cells in Ischemic Stroke Rats
Yang, M., Wei, X., Li, J.. Heinel, L. A., Rosenwasser, R., Iacovitti, L.
Cell Transplant. 19(9):1073-1084; 2010
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ZenMaster

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For more on stem cells and cloning, go to CellNEWS at
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Genomic Fault Zones Come and Go

The fragile regions in mammalian genomes thought to play a key role in evolution go through a 'birth and death' process
Wednesday, 01 December 2010

The fragile regions in mammalian genomes that are thought to play a key role in evolution go through a "birth and death" process, according to new bioinformatics research performed at the University of California, San Diego. The new work, published in the journal Genome Biology on November 30, could help researchers identify the current fragile regions in the human genome – information that may reveal how the human genome will evolve in the future.

"The genomic architecture of every species on Earth changes on the evolutionary time scale and humans are not an exception. What will be the next big change in the human genome remains unknown, but our approach could be useful in determining where in the human genome those changes may occur," said Pavel Pevzner, a UC San Diego computer science professor and an author on the new study. Pevzner studies genomes and genome evolution from a computational perspective in the Department of Computer Science and Engineering at the UC San Diego Jacobs School of Engineering.


According to research performed at UC

San Diego, the fragile regions in mammalian

genomes that are thought to play a key role

in evolution go through a "birth and death"

process. The graphic above is from the new

Genome Biology paper in which the findings

are outlined. Credit: Pavel Pevzner/

Max Alekseyev.

The fragile regions of genomes are prone to "genomic earthquakes" that can trigger chromosome rearrangements, disrupt genes, alter gene regulation and otherwise play an important role in genome evolution and the emergence of new species. For example, humans have 23 chromosomes while some other apes have 24 chromosomes, a consequence of a genome rearrangement that fused two chromosomes in our ape ancestor into human chromosome 2.
This work was performed by Pevzner and Max Alekseyev – a computer scientist who recently finished his Ph.D. in the Department of Computer Science and Engineering at the UC San Diego Jacobs School of Engineering. Alekseyev is now a computer science professor at the University of South Carolina.

Turnover Fragile Breakage Model
"The main conclusion of the new paper is that these fragile regions are moving," said Pevzner.

In 2003, Pevzner and UC San Diego mathematics professor Glen Tesler published results claiming that genomes have "fault zones" or genomic regions that are more prone to rearrangements than other regions. Their "Fragile Breakage Model" countered the then largely accepted "Random Breakage Model" – which implies that there are no rearrangement hotspots in mammalian genomes. While the Fragile Breakage Model has been supported by many studies in the last seven years, the precise locations of fragile regions in the human genome remain elusive.

The new work published in Genome Biology offers an update to the Fragile Breakage Model called the "Turnover Fragile Breakage Model." The findings demonstrate that the fragile regions undergo a birth and death process over evolutionary timescales and provide a clue to where the fragile regions in the human genome are located.

Do the Math: Find Fragile Regions
Finding the fragile regions within genomes is akin to looking at a mixed up deck of cards and trying to determine how many times it has been shuffled.


In this graphic, the coloured marks represent

positions of the putative fragile regions in the

human genome. The Turnover Fragile Breakage

Model suggests that these regions likely form

(still active) fragile regions in the human genome.

The graphic above is from the new Genome

Biology paper in which the Turnover Fragile

Breakage Model (TFBM) is presented. According

to the TFBM, the fragile regions in mammalian

genomes that are thought to play a key role in

evolution go through a "birth and death" process.

Credit: Max Alekseyev/Pavel Pevzner.

 Looking at a genome, you may identify breaks, but to say it is a fragile region, you have to know that breaks occurred more than once at the same genomic position.

"We are figuring out which regions underwent multiple genome earthquakes by analyzing the present-day genomes that survived these earthquakes that happened millions of years ago. The notion of rearrangements cannot be applied to a single genome at a single point in time. It's relevant when looking at more than one genome," said Pevzner, explaining the comparative genomics approach they took.

"It was noticed that while fragile regions may be shared across different genomes, most often such shared fragile regions are found in evolutionarily close genomes. This observation led us to a conclusion that fragility of any particular genomic position may appear only for a limited amount of time. The newly proposed Turnover Fragile Breakage Model postulates that fragile regions are subject to a 'birth and death' process and thus have limited lifespan," explained Alekseyev.

The Turnover Fragile Breakage Model suggests that genome rearrangements are more likely to occur at the sites where rearrangements have recently occurred – and that these rearrangement sites change over tens of millions of years. Thus, the best clue to the current locations of fragile regions in the human genome is offered by rearrangements that happened in our closest ancestors – chimpanzee and other primates.

Pevzner is eagerly awaiting sequenced primate genomes from the Genome 10K Project. Sequencing the genomes of 10,000 vertebrate species – including 100s of primates – is bound to provide new insights on human evolutionary history and possibly even the future rearrangements in the human genome.

"The most likely future rearrangements in human genome will happen at the sites that were recently disrupted in primates," said Pevzner.

Work tied to the new Turnover Fragile Breakage Model may also be useful for understanding genome rearrangements at the level of individuals, rather than entire species. In the future, the computer scientists hope to use similar tools to look at the chromosomal rearrangements that occur within the cells of individual cancer patients over and over again in order to develop new cancer diagnostics and drugs.

Source: University of California at San Diego
Contact: Daniel Kane

Reference:
Comparative genomics reveals birth and death of fragile regions in mammalian evolution
Max A Alekseyev, Pavel A Pevzner
Genome Biology 2010, 11:R117 (30 November 2010), doi:10.1186/gb-2010-11-11-r117
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ZenMaster

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For more on stem cells and cloning, go to CellNEWS at
http://cellnews-blog.blogspot.com/

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