Wednesday, 29 June 2011

Molecular Cartography for Stem Cells

From Cell

Researchers have long suspected that cancer cells and stem cells share a core molecular signature, but this commonality remains incompletely understood. By examining microRNA (miRNA) expression patterns in multiple types of cancer cells and stem cells, Neveu et al. (2010) have now developed the miRMap, a tool that facilitates quantitative examination of the molecular hallmarks associated with a cell's identity. Their effort resulted in a catalog of expression patterns for nearly 330 miRNAs in over 50 different human cell lines. Despite the overwhelming molecular heterogeneity among the samples, their analysis identifies 11 miRNAs that comprise a signature common to all cancer cells and shared by a subset of pluripotent stem cells. The genes targeted by these miRNAs downregulate cell proliferation or upregulate the p53 network. Although recent reports have called attention to the inherent oncogenic risk of stem cells, this new study shows that only some pluripotent stem cells look like cancer cells, and this cancer-like state cannot be predicted by a stem cell's tissue of origin or method of production. By examining the changes associated with cellular reprogramming—both when stem cells are generated from somatic cells and when induced pluripotent stem cells (iPSCs) are differentiated—Neveu et al. reveal a precise window for cancer-like behavior during iPSC generation, emphasizing that a transient downregulation of p53, rather than a complete inhibition, is required to fully reprogram somatic cells into pluripotent stem cells. Multidimensional molecular maps, such as the miRMap, help us draw a more complete picture of the events that drive the acquisition of specific cell fates during cellular reprogramming.

P. Neveu et al. (2010). Cell Stem Cell 7, 671–681.

Tuesday, 14 June 2011

Stem cells under attack

Effie Apostolou & Konrad Hochedlinger
From Nature

Induced pluripotent stem cells offer promise for patient-specific regenerative therapy. But a study now cautions that, even when immunologically matched, these cells can be rejected after transplantation.

In 2006, Takahashi and Yamanaka made a groundbreaking discovery. When they introduced four specific genes associated with embryonic development into adult mouse cells, the cells were reprogrammed to resemble embryonic stem cells (ES cells). They named these cells induced pluripotent stem cells (iPS cells). This approach does not require the destruction of embryos, and so assuaged the ethical concerns surrounding research on ES cells. What's more, researchers subsequently noted that the use of 'custom-made' adult cells derived from human iPS cells might ultimately allow the treatment of patients with debilitating degenerative disorders. Given that such cells' DNA is identical to that of the patient, it has been assumed — although never rigorously tested — that they wouldn't be attacked by the immune system. However, Zhao et al. show, in a mouse transplantation model, that some iPS cells are immunogenic, raising concerns about their therapeutic use.

Regardless of the answers to the outstanding questions, this and other recent studies reach one common conclusion: researchers must learn more about the mechanisms underlying cellular reprogramming and the inherent similarities and differences between ES cells and iPS cells. Only on careful examination of these issues can we know whether such differences pose an impediment to the potential therapeutic use of iPS cells, and how to address them. In any case, these findings should not affect the utility of iPS-cell technology for studying diseases and discovering drugs in vitro.

Nature Volume: 474, Pages: 165–166 Date published: 09 June 2011

Tuesday, 7 June 2011

Will you take the 'arsenic-life' test?

Erika Check Hayden

At first, it sounded like the discovery of the century: a bacterium that can survive by using the toxic element arsenic instead of phosphorus in its DNA and in other biomolecules.

But scientists have lined up to criticize the claim since it appeared in Science six months ago. Last week, the journal published a volley of eight technical comments summarizing the key objections to the original paper, along with a response from the authors, who stand by their work.

The authors of the original paper are also offering to distribute samples of the bacterium, GFAJ-1, so that others can attempt to replicate their work. The big question is whether researchers will grab the opportunity to test such an eye-popping claim or, as some are already saying, they will reject as a waste of time the chance to repeat work they believe is fundamentally flawed. "I have not found anybody outside of that laboratory who supports the work," says Barry Rosen of Florida International University in Miami, who published an earlier critique of the paper.

Some are also frustrated that the authors did not release any new data in their response, despite having had ample time to conduct follow-up experiments of their own to bolster their case. "I'm tired of rehashing these preliminary data," says John Helmann of Cornell University in Ithaca, New York, who critiqued the work in January on the Faculty of 1000 website. "I look forward to the time when they or others in the field start doing the sort of rigorous experiments that need to be done to test this hypothesis."

The original study, led by Felisa Wolfe-Simon, a NASA astrobiology research fellow at the US Geological Survey in Menlo Park, California, looked at bacteria taken from the arsenic-rich Mono Lake in southern California. The authors grew the bacteria in their lab using a medium that contained arsenic but no phosphorus. Even without this essential element of life, the bacteria reproduced and integrated arsenic into their DNA to replace the missing phosphorus, the paper reported.

"We maintain that our interpretation of As [arsenic] substitution, based on multiple congruent lines of evidence, is viable," Wolfe-Simon and her colleagues wrote in last week's response.

But critics have pointed out that the growth medium contained trace amounts of phosphorus — enough to support a few rounds of bacterial growth. They also note that the culturing process could have helped arsenic-tolerant bacteria to survive by killing off less well-equipped microbes.

Others say that there is simply not enough evidence that arsenic atoms were incorporated into the bacterium's DNA. The chemical instability of arsenate relative to phosphate makes this an extraordinary claim that would "set aside nearly a century of chemical data concerning arsenate and phosphate molecules", writes Steven Benner4 of the Foundation for Applied Molecular Evolution in Gainesville, Florida.

A leading critic of the work, Rosemary Redfield of the University of British Columbia in Vancouver, Canada, says that it would be "relatively straightforward" to grow the bacteria in arsenic-containing media and then analyse them using mass spectrometry to test whether arsenic is covalently bonded into their DNA backbone.

Redfield says that she will probably get samples of GFAJ-1 to run these follow-up tests, and hopes that a handful of other laboratories will collaborate to repeat the experiments independently and publish their results together.

But some principal investigators are reluctant to spend their resources, and their students' time, replicating the work. "If you extended the results to show there is no detectable arsenic, where could you publish that?" asks Simon Silver of the University of Illinois at Chicago. "How could the young person who was asked to do that work ever get a job?"

Helmann says that he is in the process of installing a highly sensitive mass spectrometer that can measure trace quantities of elements, which could help refute or corroborate the findings. But the equipment would be better employed on original research, he says. "I've got my own science to do."