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Oncolytic adenovirus

by atyy
Tags: adenovirus, oncolytic
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atyy
#1
Feb3-12, 11:25 PM
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This is a continuation of rhody's and my discussion about Clodagh O'Shea's video on using the common cold virus to target and disrupt cancer cells.

At first, I thought this corresponded to her Nature paper (free!). However, that doesn't seem to deal directly with using a virus to fight cancer, and I couldn't find anything by her about it.

However, there are some reviews:
http://www.ncbi.nlm.nih.gov/pubmed/19860656 (free!)
http://www.ncbi.nlm.nih.gov/pubmed/20463003 (free!)

The approach using p53 and a specific sort of adenovirus that replicates in and kills only tumor cells seems to go back to this paper by Bischoff et alia.

The second review indicates an alternative approach in which the virus is used to replace p53 in tumor cells. Apparently "Gene therapy using wild-type p53, delivered by adenovirus vectors, is now in widespread use in China."

Some questions, the second emphasized by rhody in the earlier thread:
1. What do we know about its effectiveness?
2. Is it safe?
3. What has O'Shea's Nature paper got to do with this?
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bobze
#2
Feb4-12, 01:08 AM
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Quote Quote by atyy View Post
This is a continuation of rhody and my discussion about Clodagh O'Shea's video on using the common cold virus to target and disrupt cancer cells.

At first, I thought this corresponded to her Nature paper (free!). However, that doesn't seem to deal directly with using a virus to fight cancer, and I couldn't find anything by her about it.

However, there are some reviews:
http://www.ncbi.nlm.nih.gov/pubmed/19860656 (free!)
http://www.ncbi.nlm.nih.gov/pubmed/20463003 (free!)

The approach using p53 and a specific sort of adenovirus that replicates in and kills only tumor cells seems to go back to this paper by Bischoff et alia.

The second review indicates an alternative approach in which the virus is used to replace p53 in tumor cells. Apparently "Gene therapy using wild-type p53, delivered by adenovirus vectors, is now in widespread use in China."

Some questions, the second emphasized by rhody in the earlier thread:
1. What do we know about its effectiveness?
2. Is it safe?
3. What has O'Shea's Nature paper got to do with this?

Sorry don't have to to look everything over tonight (slugging through pharmacology ).

To answer the second question real fast--It depends on what you mean by safe.

We cannot control where the gene is inserted by the virus, ergo you run the potential risk of creating maladaptive changes to the host cell's DNA that will ultimately lead right back to cancer.

Back when they first tried gene therapy for bubble-boy (SCID) patients this was one of the problems they encountered. After about 10 years, the patients started getting strange cancers because the replacement genes (adenosine deaminase was this particular etiology of SCIDs IIRC) could end up in the wrong spot and be carcinogenic themselves!

Here is the question though, is the juice worth the squeeze?

I'd argue in the case of bubble-boy it is. You can't live without T and B cells (the fate of people with SCID). You have a horrible short life, chalked full of opportunistic infections and normally die by the ripe age of 5. Certainly cancer as an adverse effect sucks, but we can treat the cancers at 10-15 years out, we cannot however, treat dead people.

I suppose for this query it would be based upon the prognosis and the available treatments, whether this was worth the squeeze or not. Something like 50-60% of all human cancers have mutations for p53 genes (TP53). Some of those cancers are very amendable to things like surgical resection and debridement of tumors, chemotherapy, etc. How many people do you know that have died from prostate cancer? Not many I bet, and I'd bet my prostate that going out half-cocked with an adenovirus trying to put p53 back into neoplastic prostate cells is probably a bad idea, likely to cause more morbidity and mortality than the neoplasm itself.

Got a really aggressive small cell carcinoma though? Where can I sign up doc.
atyy
#3
Feb4-12, 08:56 AM
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@bobze - thanks for the lengthy reply! But please concentrate on your pharmacology first (maybe you can find a drug to cure PF addiction )

In the case where a virus is used to insert a gene into a cell, why can't it be engineered to target a specific locus, as it can be in mice? Is the mechanism of viral insertion different from homologous recombination? Or is the virus too small to contain the longer constructs that may be needed for targeting?

Also, does this concern apply to the oncolytic adenovirus concept, where the aim isn't to replace a gene, but to kill a cell?

rhody
#4
Feb4-12, 06:28 PM
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Oncolytic adenovirus

Thanks atty, bobze,

I can't help but thinking, at the microscopic level, does the folding and twisting of DNA have anything to do with mutation of genes, by that I mean pure configuration changes ? This is a babe in the woods asking an innocent question, minus the genetic knowledge and cryptic genetic concepts and language, that geneticists speak in.

Rhody...
atyy
#5
Feb4-12, 09:59 PM
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Quote Quote by rhody View Post
Thanks atty, bobze,

I can't help but thinking, at the microscopic level, does the folding and twisting of DNA have anything to do with mutation of genes, by that I mean pure configuration changes ? This is a babe in the woods asking an innocent question, minus the genetic knowledge and cryptic genetic concepts and language, that geneticists speak in.

Rhody...
You've got an overactive imagination! "Thus, the DNA structure itself can introduce instability in a mammalian genome."

http://www.ncbi.nlm.nih.gov/pubmed/19727556 (free review!)
http://www.ncbi.nlm.nih.gov/pubmed/19066276 (free!)
http://www.ncbi.nlm.nih.gov/pubmed/16473937 (free!)
http://www.ncbi.nlm.nih.gov/pubmed/2552445 (free!)

Wikipedia gives a picture of the Z-form next to the more common B-form.
Ygggdrasil
#6
Feb5-12, 12:50 AM
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Quote Quote by atyy View Post
3. What has O'Shea's Nature paper got to do with this?
I haven't studied oncolytic adenoviruses in depth, so I can't really comment on their efficacy and safety, but I can comment on the O'Shea Nature paper. I should note prior to becomming an assistant professor at Salk, O'Shea did her postdoctoral research in Frank McCormick's lab at UCSF. McCormick's lab pioneered work on oncolytic adenoviruses (he is the senior author on the Bischoff paper you cite), so that is where she probably got interested in the topic of oncolytic adenoviruses.

The idea behind oncolytic adenoviruses is that they will specifically target cancer cells that lack functional p53. When normal adenoviruses infect cells, being DNA viruses, they require the host cells to be in S phase (the phase of the cell cycle when the cells copy their own DNA) so that they can hijack the host cell's DNA replication factors to aid in copying their own DNA. Therefore, upon infection, the viruses force the host cell to start copying its DNA. This inappropriate DNA synthesis, however, sets off alarm bells within the cell which activates the guardian of the genome, p53. Once p53 gets activated, it binds to the promoters of several genes and turns on those genes, leading to the arrest of the cell cycle or the destruction of the infected cell.

As both of these outcomes would prevent the virus from replicating and infecting other cells, adenoviruses must have some way of shutting down p53 if they wish to survive. It was thought that adenoviruses used the protein E2B-55k to do this. E2B-55k directly binds to and destroys p53. Indeed, adenoviruses lacking E2B-55k seem to be incapable of infecting cells with active p53 and can only productively infect cells lacking p53 (making this the basis for the oncolytic adenoviruses that target only cancer cells lacking p53).

Closer inspection of the engineered oncolytic adenoviruses lacking E2B-55k, however, revealed that they do not work in the way we expect. While in the McCormick lab, O'Shea discovered that the oncolytic adenoviruses selectively target cancer cells not because these cells lack p53, but because the tumor cells repair a defect in viral RNA export caused by the deletion of E2B-55k (O'Shea et al., 2004). Curiously, although p53 accumulates in cells infected by the oncolytic adenoviruses (as expected because E2B-55k is not around to destroy p53), p53 is unable to activate the proper set of genes. This result suggests that adenoviruses have additional mechanisms to inactivate p53.

Indeed, O'Shea's 2010 Nature paper identifies these additional mechanisms. Her lab finds that the adenovirus protein E4-ORF3 silences p53 activity in an unexpected way. Rather than directly binding to p53, E4-ORF3 instead goes after p53's target genes and makes them inaccessible to p53. Because p53 cannot turn on its target genes, it cannot stop viral replication, allowing the adenovirus to replicate freely and infect new cells.

In addition to uncovering a new means of regulating p53 (and providing a nice set of tools to perhaps identify new pathways cells may use to regulate p53's target genes), the research has applications toward improving oncolytic adenoviruses. Because E4-ORF3 is also responsible for inactivating p53, the paper suggests that adenoviruses engineered to be deficient in both E1B-55k and E4-ORF3 (or perhaps E4-ORF3 alone) may be more selective and more potent than the current oncolytic adenoviruses.
rhody
#7
Feb5-12, 09:10 AM
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Nice summary Ygggdrasil, your thousandth post is a memorable one, let me ask you this, I haven't read the paper, even if I did without being a molecular biologist, or a retired one for that matter, would someone such as myself, a persistent layman been able to summarize it in the way you did ? I am going to read it slowly, keeping your summary in mind to see if I follow your path or get diverted into dead ends along the way, or arrive at a different place.

Rhody...
Ygggdrasil
#8
Feb6-12, 09:02 PM
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You'll notice that of the six paragraphs I wrote about the O'Shea paper, only the last two actually discuss the findings of the paper. The first four paragraphs all describe background material. Understanding the background of a paper -- the basics of the biological system under study, the sorts of experiments that have been done before, the motivation behind the current study, and the actual question the authors of the paper are trying to answer -- is a very key part of reading a scientific paper, and understanding its significance.

For papers outside my area of expertise (such as this one), I generally first read the abstract of the paper (to know in general what the paper is studying), then pretty carefully go through the introduction of the paper, often looking up some of the most relevant papers they cite and consulting wikipedia frequently. This should hopefully give me enough background to understand the experiments they perform and their interpretation of the results.

Afterward, I usually skim though the results section, mainly looking at the subheadings, figures, and figure titles to get a general sense of the experiments they performed. Then I read through the discussion, which generally summarizes the results, gives the authors' interpretations of the results, and puts their work in the context of the broader scientific literature on the subject. If some of their interpretations seem funny, I'll sometimes go back and consult the relevant experiments in the results section.

I'll note that this is somewhat the inverse of how I read papers on topics which I have studied extensively. For these papers, I generally skim the introduction (mostly to check if they have cited studies that I am not familiar with), then read through the results section very carefully. This section often contains important details relevant to people who are actively researching a similar topic although these details may not be so important to the general reader.
rhody
#9
Feb8-12, 10:59 AM
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Quote Quote by atyy View Post
picture of the Z-form next to the more common B-form.
Thanks atty,

Once again you blew my mind: from the wiki:
For each base pair, considered relative to its predecessor, there are the following base pair geometries to consider:[21][22][23]

Shear
Stretch
Stagger
Buckle
Propeller twist: rotation of one base with respect to the other in the same base pair.
Opening
Shift: displacement along an axis in the base-pair plane perpendicular to the first, directed from the minor to the major groove.
Slide: displacement along an axis in the plane of the base pair directed from one strand to the other.
Rise: displacement along the helix axis.
Tilt: rotation around this axis.
vRoll: rotation around this axis.
Twist: rotation around the helix axis.
vx-displacement
y-displacement
inclination
tip
pitch: the number of base pairs per complete turn of the helix.
We can categorize DNA observed states/geometries fairly well, but when we ask why and start to drill down to more why's things fall apart, do they not ?

Ygggdrasil,

I am going to review the article and follow your suggested regime to see if I can grasp some of what you did, or decide if my poor brain is woefully uninformed in key critical areas.

Rhody...


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