Good Deeds

Dr. Ryan Gregory at Genomicron has posted about his father's mission to make a difference in Africa. Please take a moment to visit his site and pass along news about the effort.

Scientists Stressed About Weight Loss

Do researchers really think neuropeptide Y can sculpt the perfect body?


Every few years, researchers challenge Jenny Craig's and the late Dr. Atkins' stranglehold on the weight loss industry. (Honestly, I don't know what they are thinking. I wouldn't take Kirstie Alley on.)

I remember back around 2001 when a biotech company, Regeneron, was developing a drug trademarked as Axokine (it was actually ciliary neurotrophic factor, or CNTF) in hopes of manipulating the leptin "hunger" pathway. At the time, it was suggested that both leptin and Axokine worked in large part by inhibiting the activity of neuropeptide Y in neurons. Neuropeptide Y (NPY) was reputed to increase appetite in small animals when small doses were delivered directly to their brains. Additionally, when NPY receptor positive neurons are selectively destroyed, experimental animals eat much less. Regeneron generated data that showed that CNTF, like leptin, suppressed activity of NPY receptor positive neurons in the hypothalamus. Unfortunately for Regeneron and its stockholders in March of 2003, Phase III clinical trial results for Axokine indicated that the weight loss in the treatment group was a marginal 6.2 lbs loss. Additionally, a subset of Axokine treated patients developed antibodies to the drug which neutralized its effects. While leptin and NPY were still obvious players in appetite and weight gain/loss, it had become clear that manipulating the pathway would not be a trivial effort.

Now 4 years later, leptin and NPY are back in the news because of work published in Nature Medicine by researchers at Georgetown University Medical Center. As usual, the media has produced article titles like "Scientists Find Way to Block Weight Gain in Stressed People". (I often hate the news media, particularly FOXNews). These titles imply that overworked fat people will be able to take a pill that makes them lose weight within the next year. While there are a couple of clinical trials tied to the freshly reported research, we're going to have to wait for a little while before knowing how it will all play out. Not all of the current reports are promising. Well, let me put it this way, the research that is currently making news is right about where Regeneron was with Axokine circa 2000; and we all know how far that got.

With silly media coverage aside, the research conclusions by scientists at Georgetown University Medical Center are very interesting. It seems that NPY does not only work via appetite mediation in the brain signaling pathway. Rather, their data in mice suggest that when animals become stressed by aggression or temperature changes, their sympathetic nerves generate more NPY and NPY receptors in abdominal fat. This upregulation is concurrent with increased growth of new fat cells and in fat tissue angiogenesis . Fat tissue, just like any other tissue, needs blood supply to grow and sustain itself. The researchers backed up their conclusions further by suppressing the abdominal fat growth in stressed animals using a NPY blocker injected directly into the abdominal fat of stressed animals.

Aside from having discovered a potential way of reducing fat in the abdomen, there are other implications to this research:

1. Could anti-anxiety medications reduce this stress signaling pathway that causes weight gain?
2. Could NPY be injected to increase fat where desired? More natural looking breast implants?
3. Can increasing peripheral (outside of the brain) levels of NPY increase appetite while decreasing weight?


Major questions still remain, however. First and foremost, do human really work the same way as rodents in this case. Secondly, would this be a safe therapeutics. And, thirdly, most obviously to me, why do most of the stressed out people who I know appear emaciated. Personally, I lose weight when I get stressed. My guess is that, as usual, the physiology and molecular biology of this is far more nuanced than the current story allows. Time will tell.

Doing the Robot to a Chaotic Beat

Omnome is dedicated to talking about three broad subjects and how they intersect at the point of human application; technology. The subjects are:

• Biology
  
• Physics
• Mathematics

So far, we have talked a LOT about biology, a little about physics, and not at all about math. Honestly, it bothers me that I haven't written about math at all. Mathematics is what ties all of this together. Mathematics, by one definition, is the study of quantity, structure, space, and change. That covers a great deal since most scientific study can catagorized as the study of quantity, structure, space, and change.

In any case, I am going to introduce math to Omnome by talking about a little Japanese robot named Miuro that has a few functions. First and foremost, Miuro is a music player that can play music from an iPod or from a WiFi connection. Secondly, though, Miuro can dance. Ok, so I have watched the video, and I find Miuro's dancing to be rather lame and nondescript. It basically rolls around with a few shimmies to the beat of the music it is playing. See the video below:



Like I said, kind of lame and non-descript, right? However, the interesting thing about Miuro is that it doesn't actually have pre-programmed dance patterns. I remember very distinctly the first time I found myself almost uncontrollably tapping my feet as a young child listening to a song that came on the radio in the car. I had never learned any dance moves, yet my brain picked up a pattern in a song that made me decide to tap my feet in time with one of the song's cadences. Miuro is designed to do the same thing.

Miuro has software rooted in mathematic chaos theory that allows it to decide how to react to the music. So what is chaos theory and how would it allow a robot to "decide" anything? The study of chaos in mathematics is the study of systems with more than one changing variable that seems random, but is very much dependent on the initial conditions. Weather patterns are chaotic systems as are Earth's magnetic fields and human economies. Basically, any system that can change exponentially as a result of numerous variables in time can be considered a chaotic system. Most things still to be discovered in most fields of study will somehow be tied to these very complex systems.

So Miuro is a robot that has software that is designed to change its movement unpredicably based on: 1) The motion it is already carrying out and 2) the many musical tracks recorded in a given song 3) Where it is dancing. Any of these many variables will make Miuro decide how it wants to bust a move. Most artifical intelligence (AI) researchers believe that AI break-throughs will be ushered in via harnessing of chaotic decision making models somewhat like the Miuro model.

So this is a humble introduction to the world of Chaos Mathematics and/or Non-linear Dynamics. These are subjects of much interest to me. Unfortunately, I know very little about them right now. I am a sub-amateur student of them. I hope to change that over the coming years. I hope you, my readers, can teach me a little bit about the subjects. I hope to broach the subjects with regards to genetics, proteomics, physics, weather, disease epidemiology, and much more in the future.

Gene Swap Meet

Sorry it has been so long since our last post.

This has been a very crazy week for me that I can most aptly describe with a quote from Dr. Peter Venkman in Ghostbusters when he described "...human sacrifice, dogs and cats living together - mass hysteria!"

Anyways, I am glad the week is over. We hope to get back to more regular posting again.

While I am admittedly tired of talking about genetics here, I am going to address the subject at least 3 more times in the near future. We have two more posts to go in our State of the Art series and we have the post that I am about to write.

Currently in the news, we are hearing about steps closer to "artificial life". The idea of artificial life is an odd one to me since life can largely be catagorized as a binary state, alive or not alive. It seems difficult to me to be artificially alive. Oh, I know many of you will want to nitpick about grey areas like viruses and such, but that's a completely different question. My bottom line is that life is real or not alive. There will never be artificial life. Ah, the wonders of semantics.

So what am I talking about here? What is the big news? Researchers at the J. Craig Venter Institute in Maryland have published a paper in Science explaining how they transfered an entire genome from one species of bacteria (Mycoplasma mycoides) into a population of a completely different species of bacteria (Mycoplasma capricolum). On the surface, this might seem unremarkable since Dolly the sheep was cloned back in 1996 by transferring the entire genetic code of one sheep into a sheep egg cell. However, up until now, no cells of one species have been made to "engraft" an entirely transplanted genome of another species.

While the idea that this will lead to "artificial life" is somewhat absurd since the concept doesn't really exist, this is exciting because it could be a first step toward creating novel organisms specifically designed for a human need. Imagine a bacteria that could be designed to metabolize sugar and produce propane for fuel. While I am not sure that is an attainable endeavor, Venter seems to think it is. I imagine, to him, this publication is one more step in the right direction. Not sure it is the right direction, but it is definately a step toward his goals.

Speaking of AAV, Parkinson's Gene Therapy progress?

Considering that we've been talking about gene therapy a lot here lately, I think this news is quite relevant. Current Omnome topics aside, this news is very important.

There have been recent reports about a gene therapy strategy that resulted in symptom amelioration in Parkinson's patients. The project was spearheaded in part by Dr. Matthew During of Ohio State University. Having met Dr. During at the Society for Neuroscience conference in Orlando in 2002, I am not at all surprised that he would be part of a project that could stand at the cutting edge of clinical translational research. As a trained neurosurgeon with a PhD, this New Zealander came across as not only talented, but also as having major cojones.

So let's talk about the therapeutic that was tested by During and his colleagues. The researchers used an adeno-associated virus (AAV) to deliver a gene encoding the protein, glutamic acid decarboxylase (GAD), to the subthalamic nucleus in the brains of Parkinson's patients.

So what does that all mean? Well, let's briefly review AAV. AAV are small viruses that do not induce an immune response in humans. Additionally, they deliver DNA genetic material which directly incorporates into the cellular genome. It gets copied when transduced cells divide into daughter cells. Now we'll talk about Parkinson's Disease. Parkinson's is a complicated disease which results in neuronal death, neurodegeneration. Specific parts of the brain are very susceptible to this neurodegeneration. The substantia nigra of the brain is one of those parts. As a result the neurotransmitter balance is thrown off to the point where the substantia nigra is too "excited". The aim of a GAD gene therapy is to turn part of the substantia nigra from a primarily excitatory nucleus to a primarily inhibitory system.

Whether or not the gene therapy is working the way the researchers think it does is always up for debate. What isn't as debatable is the fact that most of the patients who received the injection of GAD encoding virus had symptomatic improvements. Since this was mainly a dose ranging and safety Phase I/II clinical trial, the number of patients was not high enough to power a statistically significant symptom amelioration metric. However, all signs point toward some hope for improved quality of life for Parkinson's patients. What this also provides is another glimmer of hope that gene therapy strategies might be in the clinic sooner than later. What this certainly is NOT is a cure. Patients need to remember that the neurons are still dying. Neurodegeneration is an extremely tough nut to crack (trust me on this one...I'm in neurodegeneration research for the long haul). Maybe one day we'll come up with a gene therapy that can protect the neurons...

State of the Art: GENE THERAPY- Pt2

See part 1

Viral Delivery

Most gene therapy strategies in research and clinical labs up until now have revolved around harnessing the evolved capabilities of viruses to deliver their viral genomes into cells. This is commonly known as use of a viral vector.

Let’s talk a little bit about viruses. Viruses are particles which can infect cells of living organisms. Viruses are made up of a protein shell encasing viral genetic material. In order to reproduce, viruses attach via their protein shells to cell surface membranes where they inject their genetic material. For normal disease causing viruses, the viral genetic material hijacks the cell’s protein and nucleotide generating machinery to produce more complete virus particles. The cycle continues until the immune system can seek and destroy the viral particles (unless the immune system is the target of the virus; as in the case of HIV). The process by which viruses deliver their viral genomes into cells is referred to as viral transduction.

In order to use a virus as a delivery vector, the viral genetic material basically needs to be removed and replaced with genetic material encoding the desired cellular product.

Retroviruses

There are a few different kinds of viruses which can be used for gene transduction. Retroviruses are one kind. Retroviruses store their genetic material in the form of RNA. When a retrovirus infects or transduces a cell, it introduces ins RNA and a few additional enzymes to the cell. The RNA is then copied to DNA inside the cell my an enzyme called reverse transcriptase. The new DNA is then inserted into the cell’s own genome by the integrase enzyme. The viral DNA is now a part of the host cell’s DNA. If the host cell divides, then any daughter cells will share the new DNA. The great thing about that from a gene therapy standpoint is the fact that there would be little or no need to introduce the therapeutic gene more than once. The downsides to it, however, are that:

1) The viral DNA can be incorporated into portions of the cell genome that result in faulty transcription of important genes. This could lead to cancer conditions caused by the gene therapy in the same way that human papillomavirus (HPV) predosiposes women for cervical cancer.

2) If the virus inserts itself into the wrong cell type, the genetic material could be passed on indefinitely within unintended cells for unintended results.

Adenoviruses

Adenoviruses are very different from retroviruses in that the genomic material which adenoviruses use to hijack a cell starts as DNA. Additionally, the DNA does not incorporate itself in the host cell’s genome. The viral DNA finds its way into the host cell’s nucleus where it is transcribed to RNA in the same way all nuclear DNA is transcribed. However, since the viral genes are not incorporated into the cell’s genome, the gene will not be duplicated and passed on to daughter cells after cell division. In one sense, this is advantageous from a gene therapists standpoint. It means that the gene product will only be produced as long as the transduced cells are alive. Long term side effects are minimal. The downside of this approach, however, is the fact that the virus would likely need to be administered more than once.

Adeno-Associated Viruses

Adeno-associated viruses (AAV) are like adenoviruses in that they carry DNA. They are like retroviruses in that the viral genomic material that they carry will be incorporated into the host cell’s genome. Daughter cells will carry the gene, but the genes will not incorporate by integrase into a random portion of the host genome. Instead, AAV always incorporates into chromosome 19. One of the biggest advantages of the AAV, however, has nothing to do with its transduction approach. AAV does not induce an immune response in humans so it can pass through the body as a vector without risk of being destroyed by T cells or macrophages. AAV will not cause fevers or inflammation when administered.

The major downside to AAV is the fact that the viral particles are very small and cannot hold very much genetic material. They would be limited in what gene products they could code for.

So now you know the three types of viruses used for gene therapies. You also know their basic advantages and disadvantages. The next installment in this series will talk about non viral gene delivery techniques. After that, we will summarize the potentially therapeutic gene products being tested in contemporary research labs. We hope you are enjoying the content so far.

State of the Art: GENE THERAPY- Pt 1

What is Gene Therapy?

Gene therapy is the term used for a biological treatment that is designed to introduce new active genetic material to living cells in order to increase or reduce a genetic product or products. These products can include either RNA or proteins or both. For the crudest of analogies, imagine the cell is a factory. This factory has assembly lines that currently build blenders. The blenders are great, but you also want to make toasters now. You send instructions to the factory to reconfigure some of its assembly lines to make toasters for at least part of the time. That is basically what is happening in gene therapy.

The most easily related example that I can think of where this technology could be useful is in Type I diabetes mellitus, where there is a deficiency in production of the protein, insulin, which is encoded by DNA on chromosome 11 in humans. An easy illustration of how a gene therapy could work would be to say that the gene for insulin production could be introduced to cells of a Type 1 diabetes patient so that their body would then be capable of generating insulin on their own. They would no longer need to take insulin shots to control high levels of blood sugar. I will stop there and now posit the emphatic caveat that the case of Type 1 diabetes is much more complex than I just described. The lack of insulin production is not because a gene is missing, rather it is because the cells that normally produce insulin are missing. In fact, diabetes might be better treated with a stem cell therapy than a gene therapy; but I digress (a topic for another State of the Art series). The main point of this ambling monologue is that, by using gene therapy, a new gene or genes can be introduced so that a cell can generate a product that it wasn’t previously generating in order to achieve a variety of net effects.

In the United States, there are currently as many as 30 clinical trials active or enrolling to test the safety and efficacy of myriad gene therapy, or gene transfer, strategies. The trials hope to find treatments for conditions ranging from X-linked Chronic Granulomatous Disease (CGD) where patients’ neutrophils cannot make a key protein necessary for infection defense to Advanced Pancreatic Cancer where a researchers are trying to test safety and dose response of delivering a “tumor killing” gene.

While there are dozens of gene therapy clinical trials and hundreds of labs worldwide conducting research with gene therapy technologies, there is still no FDA approved gene therapy product on the market; nearly 17 years after the first human gene therapy trial was conducted on a 4 year old girl with severe combined immunodeficiency (SCID) at the U.S. National Institutes of Health in 1990.

Why are gene transfers so challenging to develop and administer? There are many pitfalls. First of all, it is simply difficult to incorporate new genes into living cells, especially in a multicellular tissue system. Secondly, once the gene is there, it doesn’t always produce an active protein (or RNA). Thirdly, if the gene does work, it is very difficult, if not impossible, to turn it off, thereby rendering overdoses and immune reactions virtually impossible to treat. Forthly, it is difficult to target genes to show up in the correct cells while not also affecting cells that don’t need the gene. Lastly, there are some questions about potential to pass on the therapeutic gene to offspring who won’t need it.

These issues are currently being addressed with variable success in research around the world. They are testing many different genes and gene deliver strategies in hopes of harnessing biology’s machinery to treat diseases. In the next installments of State of the Art: GENE THERAPY, we will talk about specifics of where the technology is right now. For now, chew on this one. Think of questions. Tell me I am an idiot. Thanks for reading. :)

Upcoming Posts!

State of the Art: GENE THERAPY- Pt2
Viral Delivery

State of the Art: GENE THERAPY- Pt3
Non-Viral Delivery