General News: German E Coli Outbreak

Recent news about the German E coli O104:H4 outbreak has come back into the news, with reports of it in France and other European nations. It began when people in Germany were admitted to hospitals with bloody diarrhea in May 2011, and within a month, over 3700 cases have been reported with 42 deaths. The source of the E coli is likely to be bean sprouts according to the WHO.

E coli is a natural organism of human beings, normally residing in our gut. In fact, a very large portion of human feces is made up of E coli. They are believed to provide some health benefit to humans, perhaps by pre-binding to our intestines they prevent other bacteria from attaching to our intestinal cells. Normally E coli is harmless but sometimes, they can become pathogenic by getting infected with a virus known as a bacteriophage. This specific phage produces Shiga toxin, which is responsible for the severe diarrhea and kidney damage observed in infected patients who develop hemolytic uremic syndrome (HUS). Interestingly, this phage accidentally picked up the Shiga-toxin gene from Shigella, another pathogenic bacteria, while infecting it many years ago.

It is believed that antibiotics may be contributing to the spread of this phage, making it extremely difficult to treat patients who have this disease. Normally under non-stressed conditions, some phages lie lurking in the genome. But when bacteria are stressed by mutagens or even antibiotics, they undergo something known as the SOS response, which is essential a Hail-Mary attempt to survive. Unfortunately, this SOS response also activates the lurking phage, allowing it to exponentially divide and eventually causing the cell to burst, leaking hundreds of phage as well as Shiga toxin into the bloodstream. This is one reason why E coli infections are not usually treated with antibiotics. The other reason is antibiotics also target normal E coli in the gut, removing them and providing other bacteria the opportunity to bind and wreck havoc to the gut.

E coli also finds a home in many of the farm animals we raise, in particular cattle. It is believed that the constant application of antibiotics to cattle is contributing to pathogenic E coli. Firstly, it promotes the acquisition of multiple antibiotic resistant genes. Secondly, it promotes an explosion of phage throughout the cow gut, allowing it to infect many other E coli cells. Since cows don’t get sick from Shiga-toxin producing E coli, it is difficult to tell which cows are affected other than be testing their feces. Indeed, it has been found that over a half of cows in North America possess virulent strains of E coli.

The one thing that has people worried is that the German strain of E coli is new. While it produces Shiga-toxin, it also has multiple antibiotic resistant genes so even if we wanted to try to kill them using antibiotics, we would have a hard time doing is. In addition, bacterial species are very good at picking up genes from other bacteria, so one worry is that these antibiotic genes could transfer to a different bacteria. The other worry is that this bacteria also has some enteroaggregative E coli properties (probably from that gene swapping ability I mentioned earlier), which means it can aggregate cells on a dish. This combination of both Shiga-toxin and enteroaggregative properties has not been observed before, and so has scientists worried.

New Research: First Genome Therapy to treat Hemophilia

Hemophilia is one of the oldest genetic diseases known, famous for affecting many descendants of Queen Victoria. Back in the Babylonian times, it was described in Talmud texts that "if circumcised her first child and he died, and a second one also died, she must not circumcise her third child." Hemophilia is a genetic clotting disorder, which occurs when the gene for one of the many clotting factors is mutated. During blood-clotting, many proteins get activated which ultimately lead to formation of a net made of fibrin, trapping blood cells and forming the blood clot. In hemophilia, fibrin is no longer created so even a small bruise is extremely deadly.

These days, hemophilia is a chronic disease, treated with injections of factor into the bloodstream every other day to restore the missing protein. This is still not an optimal solution since infections can be an issue as well as possible contamination of the factor supply with disease agents (ex. AIDS). In addition, factor is extremely cost-prohibitive, costing upwards of $300,000 a year.

Since it is well known that these diseases are caused by genetic defects, adding back a functional gene should in principle cure hemophilia, the basic premise of gene therapy. However, one problem with gene therapy is how do you fix the defect. In one famous trial ten years ago, scientists added back a functional gamma-c gene to treat children with SCID-X, a disease where the immune system is so defective that children have to live in a bubble. Several of the patients began to produce functional immune system cells, curing them of SCID-X. However, several years later, two patients developed leukemia due to the yC gene being randomly inserted near the cancer-causing LMO2 gene. As a result, one goal of gene therapy today is to precisely insert the gene into the appropriate location and prevent non-random integrations.

Hojun Li from the High lab at the Children's Hospital of Philadelphia described a potential cure for hemophilia B, caused by a mutation in Factor 9 (F9). In it, they use the technique of zinc-finger nucleases developed in California by Sangamo. Zinc-fingers are a structure in proteins that recognize specific sequences in DNA. If one strung together a bunch of zinc-fingers, one can make it bind to a specific spot in the genome. Now if we add on an enzyme that cuts DNA called a nuclease, one creates a nick at a very specific spot in the genome. If one then adds in a copy of the functional gene, it can be swapped into the genome through a process called homologous recombination.

Li took mice engineered to have a F9 mutation and infected them with two viruses, one containing the zinc-finger nuclease and another containing the functional copy of the gene. The specific virus strain they used (hepatotropic adeno-associated virus) specifically infects liver cells, the site where clotting factors are made in people. After a few weeks post-treatment, they discovered that the liver was now producing functional F9 and the mice could now clot blood. More importantly, they found the functional gene copy inserted precisely into site of interest and no-where else. Not only were these mice “cured” of hemophilia, the dangers discovered with the SCID-X trial indicated above should not occur in these mice.

This is a promising study. One can foresee a quick movement towards clinical trials and treatments in humans, especially because these mice engineered to use human variants of F9. If this method is found to be safe, zinc-finger nucleases may become the norm for treating many genetic diseases. Indeed, one could say that hemophilia may become the first genetic disease officially cured.



Li H, et al. (2011) In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature, [Epub ahead of print Paper.

Cavazzana-Calvo, M., et al. (2000) Gene therapy of human severe combined immunodeficiency (SCID)-X1 disease. Science, 288(5466):669-72. Paper

Q&A: Stem Cell Revolution

Q&A: I have heard for several times in the last few years about some stem cell revolution. Apparently we no longer need to use embryonic stem cells anymore. I was wondering if you could explain this. Thanks, Jennifer


Hi Jennifer,

It sounds like they are referring to induced pluripotent stem (iPS) cells. It is rare that we see true breakthroughs in science where one paper can shock the world, but this discovery was one of them.

For the longest time, embryonic stem cells (ESCs) were considered the holy grail of stem cells. They are pluripotent stem cells because they give rise to all the cells in an adult being but not to the placenta or amniotic sac. Due to this ability, stem cell researchers dreamed of a future where one could take an embryonic stem cell and turn it into the appropriate cell type when needed: new β-cells if the pancreas failed, new neural stem cells upon paralysis or stroke, new cardiomyocytes after a heart attack. The implications were enormous. The problem was that we needed embryonic stem cells.

Embryonic stem cells are not without controversy, the first reason being that the process of harvesting the embryonic stem cells prevents the embryo from ever going to term. The other problem with embryonic stem cells is that they derive from another embryo that is not yourself, so even if the desired cells could be generated, one could still have transplantation issues where your immune system recognizes it as foreign and thus, attacks it.

And then, in 2006, Yamanaka's group made a big discovery. He could take a type of skin cell called the fibroblast and "re-program" them back into an embryonic stem cell state through some molecular magic. Let me repeat that once again. One can turn a skin cell into an embryonic stem cell. Somehow, four genes (Oct4, c-Myc, Sox2 and Klf4) could turn off the skin cell instructions and turn on the embryonic stem cell instruction.

This shocked the world. No one really believed it at first. For the longest time, scientists have always believed in the unidirectional flow of development; for instance, a fertilized egg begets ESCs, which begets ectodermal cells, which begets skin precurors, which begets fibroblasts. A fibroblasts never went back to become an ESC; it only went the other way. However, Yamanaka demonstrated cells were actually plastic. It has been replicated hundreds of times (I've turned a skin cell into an embryonic stem cell), and not only that, this molecular magic isn't specific to only creating ESCs. One can turn skin cells to neurons, to heart cells, and even to liver cells, by using a different cocktail of genes.

And so with one paper, the issues of harvesting embryos for their embryonic stem cells or that of tissue rejection are non-issues. Currently, scientists are assessing the safety of these cells and trying to understand how this reprogramming actually happens. But let us imagine a future where your liver is beginning to fail. You go to a clinic and the doctor takes a skin biopsy. Then, in a lab somewhere, those skin cells are turned into embryonic stem cells, grown into large numbers, and then changed once again to liver cells. After, they then replace your damaged liver cells with these newly made cells. This may seem like a sci-fi story but it is finally getting within reach.

Takahashi, K., and Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676. Paper

New Research: Reversing Aging

One inevitable fact of life is that we age. As we get older, our skin gets less elastic, our hair colour begins to grey and our bodies don't function as well as they used to. Our cells can only divide a certain number of times, after which, they die. If I placed a photo of a 50 year old male and a 20 year old male, you'd no doubt be able to distinguish the two individuals. Yet a baby from a 50 year old man looks the same age as a baby from a 20 year old man. Somehow the characteristics we associate with aging aren't conveyed to our offspring. So somewhere in the process of creating a baby, aging is reset.

Yeast cells also age, with several hallmarks of aging visible under a microscope. Like humans, as cells age, proteins begin to form clumps in the cells, which can impede cellular function. Accumulation of proteins is one of the major symptoms in neurodegenerative diseases like Alzheimer's or Parkinson's Disease. In addition, aged yeast cells accumulate extrachromosomal ribosomal DNA circles (ERCs) in their body. The nucleolus – the part of the cell that produces factories for making proteins – begins to look abnormal as cells age. Moreover, older yeast cells contain more bud scars (a consequence of cell division) than daughter cells; talk about a traumatic birth!

Elçin Ünal from the Amon lab at MIT set out to investigate this phenomenon in yeast: why is it that aging characteristics aren't conveyed to the next generation? She found that that yeast reset their age during the process of forming spores, which are the yeast equivalent of sperm or egg. Before forming spores, he saw those hallmarks of aging in yeast cells yet subsequent to sporulation, many of those hallmarks were gone. Those protein blobs were eliminated, likely due to autophagy, a cellular process that degrades the cell's own components. In addition, the ERCs were now eliminated from spores.

They found a gene, Ndt80, was activated as the aging reset was occurring. In fact, when they forced the gene to turn on in old yeast cells, it could significantly extend the old yeast-cells lifespan! What is Ndt80? Ndt80 is something called a transcription factor; it functions as a switch to turn on many other genes in the cell. Strangely, turning on this gene in old cells only causes the abnormal nucleolar structure to be fixed, yet this is enough to cause the cells to live twice as long. This could mean that one major cause of aging is nucleolar damage.

In summary, the Amon lab found a gene linked with resetting aging during the formation of children. Turning on Ndt80 in old cells was enough to make them live longer. The next steps would be to see whether this process holds for mice and humans. Humans do have a gene related to Ndt80. Interestingly, this gene is turned on in a cell-type that doesn't age, cancer cells, which further suggests that the anti-aging process may hold true in humans. If it is true, one can envision that turning on Ndt80 in humans may prevent aging.


Unal, E., Kinde, B., and Amon, A. (2011). Gametogenesis Eliminates Age-Induced Cellular Damage and Resets Life Span in Yeast. Science. 332, 1554-7. Paper