Prof R Virology blog on XMRV integration in prostate cancer

urbantravels

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More detail on the 2008 prostate cancer study showing proviral integration that Eric Silverman of the Cleveland Clinic had referred to in the comments on an earlier posting.

http://www.virology.ws/2011/01/04/retroviral-integration-and-the-xmrv-provirus/

A strong argument that the novel human retrovirus XMRV is not a laboratory contaminant is the the finding that viral DNA is integrated in chromosomal DNA of prostate tumors. Why does this result constitute such strong proof of viral infection?

....

To identify XMRV proviral DNA, genomic DNA was isolated from prostate tumors, and DNA was amplified using a primer that annealed in the viral env gene, near the right-hand LTR. Nucleotide sequence analyses of amplified DNAs from 14 different patients showed the expected viral CA sequence followed by human DNA. However, the other cardinal sign of retroviral integration duplication of host DNA sequences flanking the integration site could not be confirmed, because only the right-hand integration site was studied.

The isolation of the entire proviral DNA, including both flanking integration sites, from patients with prostate cancer or chronic fatigue syndrome would be additional evidence that XMRV is a virus that infects humans.
 

Cort

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Apparently Racaniello wants more evidence...I thought viral integration would be enough.. from the blog

Viral Integration into the Human Gene....1/2 Way There - Dr. Racaniello gave us a science lesson on viral integration in his Virology Blog. We keep hearing that viral integration into the human genome will go a long way to lay to rest some researchers fears about XMRV. It turns out that viral integration is just like it sounds. Once a virus gets into a cell it uses an enzyme called reverse transcriptase to turn its single-stranded RNA genome into the double-stranded DNA used by our cells. Then it uses an enzyme called integrase to integrate the viral DNA into our DNA. How to confirm this has happened? 'Simply' amplify the viral DNA sequences and determine if they are bordered by human DNA. ('Simply' may considerably understate the complexity of this task since it has not occurred with ME/CFS yet and only partially prostate cancer). If viral DNA is bordered by human DNA you have evidence that the virus has entered a human cell and burrowed into human DNA. At that point it doesn't matter where the virus came from; it's now infected a human cell and is now an infectious human virus.

Why is XMRV only halfway there? Because the Silverman team proved that one side of the virus was bordered by human DNA but not the other. Although they were able to show human DNA was present in every sample, and if one side is integrated in human DNA, it would seem strange that the other side wouldn't be, Dr. Raccaniello wants more.

The isolation of the entire proviral DNA, including both flanking integration sites, from patients with prostate cancer or chronic fatigue syndrome would be additional evidence that XMRV is a virus that infects humans.​

Finding XMRV was integrated into human DNA would still apparently not clinch it for Dr. Racaniello - note that he'll only go so far as to say 'it would be additional evidence'...One wonders what would clinch XMRV being a human infectious virus for him (and I will ask in his blog).

Down the Rabbithole - Dr. Alan Dove, in a comment posted to the blog, wants to dot even more i's and cross some more t's. He stated that

Besides looking at the other end to check for duplication, I'd also want to see some blinded samples from healthy controls. That's especially important in this case, as they're doing a preliminary linear amplification on the patient samples before doing the junction PCR. With that much amplification, and with the first step open-ended, I think there's some room for PCR artifacts.