Absence Makes the Heart Grow Fonder

It has been far too long since I last posted. I have missed the Omnome project and the Science Blogging community as a whole quite a bit while I have been distracted. I realized in the first months after initiating this blog site that the diversity of discussion in the science blog community really expanded my scientific thinking.

I hope my experiences in the past few weeks that have caused me to be so absent from Omnome will have provided me some insights that will enrich my posts on a few subjects that are regularly addressed here.

So what have I been doing? First of all, to say that I have been doing anything is a gross overstatement as anything I do is as part of a massive team effort. Secondly, I am somewhat constrained by organizational confidentiality agreements so it would be unprofessional for me to say too much. However, I think I can safely tell you the following about my past month:

1) Data was finally compiled and made accessible to me from a very large gene expression profiling effort which took my group one full year to complete. The dataset is made up of about 9 million data points. Mining is fun! Spotfire software can be fun as a visualization tool of the data. However, the statistical power of the program is sorely lacking.

2) My research group used stem cells in an animal model of neurodegeneration. I am pretty sure that's all I can really say about that. However, I suspect I will interject more thoughts about the technology in future posts as a result of my experiences with these cells.

3) My research group has initiated two large scale gene therapy efforts in animal models of neurodegeneration using adenoviral vectors.

I hope I will be able to find the time to frequent Omnome a bit more again. I look forward to visiting my scienceblogs favorites again as well. However, the people who actually pay me at work will continue to have a say over that.

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