Archive for May, 2009

Stem cell discussion at BIO convention

The public’s expectations for advances and cures in the stem cell field are ahead of reality, biotechnology executives and venture capitalists said Monday.

I attended a discussion at the BIO convention now underway in Atlanta on stem cell technology. It was worthwhile to get an idea what top industry people are saying, even if there wasn’t a ton of breaking news.

Scientists are forging ahead, most obviously with the recent discovery that it is possible to convert differentiated cells back into stem cells without introducing new DNA. Still, regulatory, patent and financial issues will probably slow the clinical development of stem cell technology over the next decade, said venture capitalist Steve Burrill, part of a four-member panel at BIO Monday.

Every company smaller than $1 billion, and that includes much of the field, the capital markets will neglect, Burrill said.

“These are some of the most complex biologics anyone has worked with. Cells are just going to be harder,” said Richard Gregory of Genzyme.

Other panelists: Paul Grayson of Fate Therapeutics, Ian Ratcliffe of StemGent

Outside the United States, desperate patients are being offered unproven stem cell “treatments” as a way to treat several neurological diseases. Someone on the panel (Gregory?) said he’d been to Beijing and was apprehensive about possible outcomes. But at the same time, some US companies may look to more flexible regulatory regimes as a way around a conservative FDA.

Some suggested that a field emphasizing transdifferentiation, directly converting one type of donated differentiated cells from patients into another that can be used for therapy, may grow out of the stem cell field. (Harvard’s Doug Melton was mentioned reverently.) This would have the advantages of avoiding early-stage embryos and probably reduce the ability of introduced cells to cause tumors.

Moderator Aaron Rowe, a writer with Wired, at one point asked the panel “How would you reform the FDA,” since the regulatory environment was so uncertain.

Panelists discussed the wisdom of allowing patients to take on considerable risks of volunteering for stem cell trials. Although I did not mention it during the discussion, I worry about a potential Jesse Gelsinger scenario. If a patient dies, everyone will ratchet back risk, even if he/she could grasp what he was getting into.

James Wilson makes this point in an essay in Science. Well worth reading.

(Commentary on Wilson)

Burrill had a elegant summary, saying that AIDS activists had changed the risk vs reward profile of clinical research, allowing patients in urgent need to take on more risk. Then Vioxx came along and made the FDA and industry more conservative, swinging the pendulum back.

Rowe tried to get panelists to come up with a two-word catchy phrase describing small molecules that can guide stem cell differentiation. He conjured up an image of postdocs poring over heat maps, playing the appropriate signaling pathways like violinists, but the panel rejected this picture as too ambitious.

Some of the products the panelists discussed:

Genzyme’s Mozobil, a stem cell mobilizer

Fate Therapeutics is planning a phase Ib trial for a small molecule that could aid homing by stem cells in bone marrow transplants.

Technology challenges discussed:

Growing pluripotent cells in suspension culture (without feeder cells) – I don’t know if this is really possible, because stem-ish cells will always need various ligands, properly arranged, to make them happy. Maybe some kind of artificial matrix.

I would add: quality control assays to ensure that a batch of cells is not tumorigenic, isn’t missing chromosomes, stuff like that.

The San Diego Biotechnology Network’s blog also has a post about the same session from Mary Canady, emphasizing Fate Therapeutics more.

Leave a Comment

The blue whales of crystallography

Fun tour through the big protein complexes crystallographers are stalking these days, such as ribosome, spliceosome, nuclear-pore, HIV trimer, G-protein coupled receptor…

Leave a Comment

Wow: a VDJ crystal structure!

Recently my heart was filled with joy to see a paper published by the laboratory where I did my PhD.

David Schatz’s lab at Yale has obtained a crystal structure of part of the protein RAG-1 bound to DNA. My congratulations to first author Fang Fang Yin.

RAG-1 and its sister RAG-2 form the scissors that cut the DNA in immature white blood cells during VDJ recombination, a process where the developing immune system slices and reassembles antibody genes in a unique, partly random way.

Because VDJ recombination can happen in a different way in each cell, the immune system has a library of millions of antibodies that can react with many different antigens out in the environment.

The signals on the DNA that mark off the gene segments that get cut and pasted together again come in two flavors. They look like this:

Antibody gene segment — CACAGTG – 12 letters – ACAAAAACC


Antibody gene segment — CACAGTG – 23 letters – ACAAAAACC

The puzzle that attracted me to this area of research was this: the RAGs need one of each kind, 12 and 23, to cut the DNA. That’s weird.

Another weird aspect is that the part of the DNA opposite the CACAGTG is turned into a hairpin, with one strand of the DNA double-helix joined to the other.

We can imagine a process like this: the RAG proteins grab one of each signal and pull them together, forming a loop. What do the proteins look like when this loop forms? What are the geometric requirements for assembling this complex?

These are the questions I was trying to answer, or at least move closer to answering, during my PhD research.

Besides being a fascinating puzzle and the centerpiece of the adaptive immune system, VDJ recombination has connections to:

  • DNA repair, because all sorts of monkey wrenches can interfere with the immune system’s ability to smush the DNA back together again
  • Evolution, because the transposon-like arrangement suggests how antibodies suddenly appeared in vertebrate biology millions of years ago

When I started it hadn’t rigorously been proven that the RAGs actually cut DNA directly. With the help of Thomas Leu, a postdoc from Switzerland, I put together a system for examining how they cut DNA in the test tube. I also did some experiments where I crosslinked the RAGs to the DNA with UV light.

But actually getting a crystal structure, that’s really impressive and difficult. Now David’s group (and other scientists) can start to build a model of the whole complex.

X-ray crystallography might not allow visualization of an entire ready-to-cut structure with both 12 and 23 signals because the whole shaky bridge might be too flexible for crystals to form.

The structure published in Nature SMB doesn’t include the CACAGTG part, which is where the DNA gets cut, or RAG2, which is necessary for cleavage to occur.

But it does show that two RAG proteins intertwine and that unit binds to two separate ACAAAACC elements at once. That’s a great step forward.

Leave a Comment