Wednesday, 22 June 2011

Stem Cell Model of Inherited ALS

Offers clues to cause of the disease
Wednesday, 22 June 2011

An international team of scientists led by researchers at the University of California, San Diego School of Medicine, have used induced pluripotent stem cells (iPSCs) derived from patients with amyotrophic lateral sclerosis (ALS). This work reveals for the first time how reduced levels of a specific protein may play a central role in causing at least one inherited form of the disease.

The work, published in the June 2011 online issue of the journal Human Molecular Genetics, could help scientists overcome a major hurdle in the study and treatment of ALS, an incurable neuromuscular disorder also known as Lou Gehrig's disease. ALS is universally fatal, with a median age of onset of 55 years and survival of two to five years after symptoms appear. Past research efforts have long been stymied by difficulties in translating successful drug tests in animal models of ALS to humans.

"There is an urgent need for ALS human models that can be translated into clinical trials to verify therapeutic targets in the human genetic background," said Alysson R. Muotri, PhD, assistant professor in the UCSD Departments of Pediatrics and Cellular and Molecular Medicine, and one of the study's senior authors.

"Rodents have been used in the past and still have a critical impact in unveiling the complexity of ALS, but the vast majority of drugs that have demonstrated efficacy in rodent models have not done the same in preclinical and clinical human trials."

In the new work, Muotri and colleagues turned to iPSCs derived from the skin cells of patients with a familial form of ALS called ALS8 to create motor neurons that provided a novel in vitro model of the disease. iPSCs from ALS patients have been described before, but finding cellular and molecular phenotypes has proved to be a continuing challenge. The use of a familial form of ALS offered an advantage since the mutated gene could be tracked during motor neuron differentiation.

"We don't know what causes most cases of ALS, but for roughly 10 percent of patients with ALS, the disease is the result of inherited genetic mutations," Muotri said.

"One of these familial forms is ALS8, which results from mutations in the VAPB gene. Using iPSCs from several patients from two independent families, we found that VAPB protein levels are reduced in ALS8-derived motor neurons compared to similar cells from non-carrier siblings of ALS8 patients."

Muotri said the finding suggests reduced VAPB protein levels may be a key to the development of ALS8 and perhaps other forms of the disease as well, including sporadic or non-hereditary ALS, where reduced VAPB protein levels have also been documented.

"The VAPB protein is involved in many cellular processes, so it seems likely it contributes to the pathogenesis of other forms of ALS," Muotri said.

"We don't yet know how the loss of VAPB is involved in causing familial or sporadic ALS, but the new ability to study this disease in human cells provides an unprecedented opportunity to answer that question, to develop new early diagnostic tools and to identify new targets for future drugs and therapies."

About ALS
Amyotrophic lateral sclerosis is a rapidly progressive, invariably fatal neurological disease that attacks the neurons responsible for controlling voluntary muscle movement. It does not generally impair cognitive function. An estimated 20,000 to 30,000 Americans have ALS, with 5,000 new cases diagnosed each year. ALS strikes most commonly between the ages of 40 and 60, affecting men more often than women, but with no distinction of race or ethnic background. In 90 percent of all ALS cases, the disease appears to occur randomly without clearly associated risk factors. Ten percent of cases are inherited, due to gene mutations.

Source: University of California at San Diego
Contact: Scott LaFee

Downregulation of VAPB expression in motor neurons derived from induced pluripotent stem-cells of ALS8 patients
Miguel Mitne-Neto, Marcela Machado-Costa, Maria C. N. Marchetto, Mario H. Bengtson, Claudio A. Joazeiro, Hiroshi Tsuda, Hugo J. Bellen, Helga A. C. Silva, Acary S.B. Oliveira, Monize Lazar, Alysson R. Muotri, and Mayana Zatz Hum. Mol. Genet. (2011) ddr284 first published online June 17, 2011 doi:10.1093/hmg/ddr284


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Monday, 13 June 2011

We Are All Mutants

First direct whole-genome measure of human mutation predicts 60 new mutations in each of us
Monday, 13 June 2011

Each one of us receives approximately 60 new mutations in our genome from our parents.

This striking value is reported in the first-ever direct measure of new mutations coming from mother and father in complete human genomes published today.

For the first time, researchers have been able to answer the questions: how many new mutations does a child have and did most of them come from mum or dad? The researchers measured directly the numbers of mutations in two families, using whole genome sequences from the 1000 Genomes Project. The results also reveal that the forces of mutation change human genomes, like all genomes: our DNA is altered by differences in its code from that of our parents. Mutations that occur in sperm or egg cells will be 'new' mutations not seen in our parents.

Although most of our variety comes from reshuffling of genes from our parents, new mutations are the ultimate source from which new variation is drawn. Finding new mutations is extremely technically challenging as, on average, only one in every 100 million letters of DNA is altered each generation.

Previous measures of the mutation rate in humans has either averaged across both sexes or measured over several generations. There has been no measure of the new mutations passed from a specific parent to a child among multiple individuals or families.

"We human geneticists have theorised that mutation rates might be different between the sexes or between people," explains Dr Matt Hurles, Senior Group Leader at the Wellcome Trust Sanger Institute, who co-led the study with scientists at Montreal and Boston.

"We know now that, in some families, most mutations might arise from the mother, in others most will arise from the father. This is a surprise: many people expected that in all families most mutations would come from the father, due to the additional number of times that the genome needs to be copied to make a sperm, as opposed to an egg."

Professor Philip Awadalla, who also co-led the project and is at University of Montreal explained:

"Today, we have been able to test previous theories through new developments in experimental technologies and our analytical algorithms. This has allowed us to find these new mutations, which are like very small needles in a very large haystack."

The unexpected findings came from a careful study of two families consisting of both parents and one child. The researchers looked for new mutations present in the DNA from the children that were absent from their parents' genomes. They looked at almost 6000 possible mutations in the genome sequences.

They sorted the mutations into those that occurred during the production of sperm or eggs of the parents and those that may have occurred during the life of the child: it is the mutation rate in sperm or eggs that is important in evolution. Remarkably, in one family 92 per cent of the mutations derived from the father, whereas in the other family only 36 per cent were from the father.

This fascinating result had not been anticipated, and it raises as many questions as it answers. In each case, the team looked at a single child and so cannot tell from this first study whether the variation in numbers of new mutations is the result of differences in mutation processes between parents, or differences between individual sperm and eggs within a parent.

Using the new techniques and algorithms, the team can look at more families to answer these new riddles, and address such issues as the impact of parental age and different environment exposures on rates of new mutations, which might concern any would-be parent.

Equally remarkably, the number of mutations passed on from a parent to a child varied between parents by as much as tenfold. A person with a high natural mutation rate might be at greater risk of misdiagnosis of a genetic disease because the samples used for diagnosis might contain mutations that are not present in other cells in their body: most of their cells would be unaffected.

Source: Wellcome Trust Sanger Institute
Contact: Don Powell, Press Officer

Variation in genome-wide mutation rates within and between human families
Donald F Conrad, Jonathan E M Keebler, Mark A DePristo, Sarah J Lindsay, Yujun Zhang, Ferran Casals, Youssef Idaghdour, Chris L Hartl, Carlos Torroja, Kiran V Garimella, Martine Zilversmit, Reed Cartwright, Guy A Rouleau, Mark Daly, Eric A Stone, Matthew E Hurles & Philip Awadalla for the 1000 Genomes Project
Nature Genetics, published online 12 June 2011, doi:1038/ng.856

See also:
We Are All Human Mutants
Measurement of mutation rate in humans by direct sequencing
CellNEWS - Thursday, 27 August 2009


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Friday, 10 June 2011

New Genetic Technique Converts Skin Cells into Brain Cells

New Genetic Technique Converts Skin Cells into Brain Cells
Friday, 10 June 2011

A research breakthrough has proven that it is possible to reprogram mature cells from human skin directly into brain cells, without passing through the stem cell stage. The unexpectedly simple technique involves activating three genes in the skin cells, genes that are already known to be active in the formation of brain cells at the foetal stage.

The new technique avoids many of the ethical dilemmas that stem cell research has faced.

For the first time, a research group at Lund University in Sweden has succeeded in creating specific types of nerve cells from human skin. By reprogramming connective tissue cells, called fibroblasts, directly into nerve cells, a new field has been opened up with the potential to take research on cell transplants to the next level. The discovery represents a fundamental change in the view of the function and capacity of mature cells. By taking mature cells as their starting point instead of stem cells, the Lund researchers also avoid the ethical issues linked to research on embryonic stem cells.

Head of the research group Malin Parmar was surprised at how receptive the fibroblasts were to new instructions.

“We didn’t really believe this would work, to begin with it was mostly just an interesting experiment to try. However, we soon saw that the cells were surprisingly receptive to instructions.”

The study, which was published in the latest issue of the scientific journal PNAS, also shows that the skin cells can be directed to become certain types of nerve cells.

In experiments where a further two genes were activated, the researchers have been able to produce dopamine brain cells, the type of cell which dies in Parkinson’s disease. The research findings are therefore an important step towards the goal of producing nerve cells for transplant, which originate from the patients themselves. The cells could also be used as disease models in research on various neurodegenerative diseases.

Unlike older reprogramming methods, where skin cells are turned into pluripotent stem cells, known as IPS cells, direct reprogramming means that the skin cells do not pass through the stem cell stage when they are converted into nerve cells. Skipping the stem cell stage probably eliminates the risk of tumours forming when the cells are transplanted. Stem cell research has long been hampered by the propensity of certain stem cells to continue to divide and form tumours after being transplanted.

Before the direct conversion technique can be used in clinical practice, more research is needed on how the new nerve cells survive and function in the brain. The vision for the future is that doctors will be able to produce the brain cells that a patient needs from a simple skin or hair sample. In addition, it is presumed that specifically designed cells originating from the patient would be accepted better by the body’s immune system than transplanted cells from donor tissue.

“This is the big idea in the long run. We hope to be able to do a biopsy on a patient, make dopamine cells, for example, and then transplant them as a treatment for Parkinson’s disease,” says Malin Parmar, who is now continuing the research to develop more types of brain cells using the new technique.

Source: Lund University
Contact: Malin Parmar

Direct conversion of human fibroblasts to dopaminergic neurons
Ulrich Pfisterer, Agnete Kirkeby, Olof Torper, James Wood, Jenny Nelander, Audrey Dufour, Anders Björklund, Olle Lindvall, Johan Jakobsson, and Malin Parmar
PNAS 2011; 6 June 2011, doi: 10.1073/pnas.1105135108


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Thursday, 9 June 2011

Curtailing Embryonic Stem Cell Research Would also Hurt iPS Cell Research

Curtailing Embryonic Stem Cell Research Would also Hurt iPS Cell Research
Thursday, 09 June 2011

Stanford bioethicist Christopher Scott.
Any legislation that slows human embryonic stem cell research is likely to also seriously harm the study of induced pluripotent stem cells, according to a new study by researchers at the Stanford University School of Medicine, the Mayo Clinic and the University of Michigan.
The finding strongly refutes the idea that embryonic stem cell research can be abandoned in favour of the less-controversial iPS cells, which are derived from adult human tissue.

"If federal funding stops for human embryonic stem cell research, it would have a serious negative impact on iPS cell research," said Stanford bioethicist Christopher Scott, citing a "false dichotomy" between the cell types.

"We may never be able to choose between iPS and ES cell research because we don't know which type of cell will be best for eventual therapies."

Scott, who directs Stanford's Stem Cells in Society Program, is the first author of the study, which compared the patterns of scientific publication on human embryonic and induced pluripotent stem cells. The study will be published in the June 10 issue of Cell.

The researchers also concluded that human embryonic stem cell research does not siphon federal funding away from studies of iPS cells, as has been claimed by the two plaintiffs in an ongoing Washington, D.C., district court case under consideration by Judge Royce Lamberth. Instead, studies of the two types of stem cells are likely to occur in tandem as established embryonic stem cell researchers rush to buffer themselves against a possible loss of federal funding.

"We're finding that scientific decisions are being made not because of science, but in response to other constraints, such as which cell types qualify for federal funding, how many lines are available and which can be obtained quickly and easily," said Scott.

As a result, the fields have become so tightly intertwined as to be inseparable; any loss of funding for these researchers will negatively impact all the work in their labs, including iPS cell research, Scott and his colleagues conclude.

Unlike embryonic stem cells, which are derived from human embryos, iPS cells can be created from adult tissue such as skin cells. They look and act like embryonic stem cells, but recent research has suggested that there are significant differences between the two cell types that may affect how they can be used for research and eventual human therapies.

In 2001, then-President George W. Bush restricted the use of federal funds to research on human embryonic stem cell lines derived before Aug. 9 of that year; in March 2009, President Barack Obama reversed that decision to allow research on many more cell lines. However, the legality of federal funding for human embryonic stem cell research is now being considered in the ongoing district court case filed in August 2010.

Scott and his colleagues, including senior author Jason Owen-Smith, PhD, associate professor of sociology and of organizational studies at the University of Michigan, analyzed more than 2,000 scientific papers published between 2007, when iPS cells were first reported, and 2010. They compared how many papers described research using exclusively human ES cells, human iPS cells, or both ES and iPS cells.

"It's always really interesting to look more closely at things that appear in the popular press," said Scott.

"We've been hearing that, since we now have iPS cells, we don't need to continue embryonic stem cell research. There's a perception that iPS cells are 'democratizing' the field because they are fairly straightforward to work with from a technical point of view."

The analysis of published papers tells a different story. Scott, Owen-Smith and their colleagues found that the iPS field is dominated by well-established, senior hES cell researchers. Many of these researchers are publishing studies that directly compare hES cells with iPS cells, rather than focusing exclusively on one cell type.

"Although we did see a very rapid uptake of iPS cell technology during the first three years, we didn't find many new researchers moving into the field," said Scott.

"The scientists who are adopting iPS quickly are the usual suspects. The old guard is working furiously to develop new iPS cell lines."

The researchers found that the original two papers in 2007 describing the creation of iPS cells had blossomed to 158 papers focused on iPS cells in 2010. In contrast, human embryonic stem cell technology was adopted much more slowly, from the first paper in 1999 to just 12 papers in 2001. Although the prior hES cell research made the adoption of iPS cell research easier, Scott and his colleagues attribute the difference in uptake of technologies to be primarily policy-driven, as researchers increasingly began to look for alternatives to the politically controversial hES cells.

However, stem cell scientists are not abandoning hES cells in favour of iPS cells. In 2008, only three of the 15 iPS cell papers (5 percent) published also reported hES cell results; in 2010, 98 of the 158 iPS cell papers (about 26 percent) did so.

"The incentives to use both types of cell in comparative studies are high because the science behind human iPS cells is still in its infancy," Owen-Smith said.

"As a result, induced pluripotent stem cells do not offer an easy solution to the difficult ethical questions surrounding embryonic stem cell research."

Scott and his colleagues also directly polled stem cell researchers at the 2010 annual meeting of the International Society for Stem Cell Research, which was held in San Francisco, as to their choice of cell lines, and compared patterns of collaboration in the iPS and hES cell fields. They found that, between 2008 and 2009, 55 senior authors (those listed as last authors) published papers using both hES and iPS cells. Only 14 of the senior authors published papers using iPS cells alone. The finding suggests that iPS cell technology has not been as widely disseminated as may have been expected and that senior researchers vulnerable to legislative changes affecting ES cell research continue to dominate the field.

"The deeper implications of a federal ban or restrictions on hES cell research are largely missing from the policy discussion surrounding the Lamberth decision," they write.

"We now have clear evidence showing the real possibility of collateral damage caused by ill-conceived and politically motivated policy prescriptions. Restrictions, regulatory uncertainty and spurious court decisions have undoubtedly retarded progress in the pluripotent stem cell field. Now, an entirely new technology, forged out of the crucible of political controversy, stands at risk."

Source: Stanford University Medical Center
Contact: Krista Conger


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