Comments

1. #1 gf1

   March 5, 2010

   Understanding this is all very provisional, and no-one’s going to really know, I’ve got a couple of Qs (you said I should ask):

   Does this make it unlikely that XMRV is related to prostate cancer, as well as CFS? I’ve read a few things which seem to now assume XMRV can infect humans, even if we don’t know what this might lead to – would this new paper make you think that this is probably not the case? (Assuming it’s right). Would cancerous cells have these defenses too?, ie: could the link between XMRV and cancer just be that cancerous cells lack the natural defenses to the virus (I don’t know how the virus would get to these cells though?)

   Does this mean that, if XMRV can infect people, our natural defenses would be far more likely to be able to fight off an infection, rahter than it necessarily being life-long?

   Would any of this have any implications for the varying results we’ve seen with CFS and prostate cancer? (Implying either that it would be unusually difficult to detect in patients, or that the positive results were likely to have been mistaken).

   Ta.

2. #2 qetzal

   March 5, 2010

   Adding to gf1′s questions:

   - Are there normal (non-cancerous) human cell types that are known to lack significant APOBEC3G & Tetherin activity?

   - Would the activation procedures that WPI used when culturing PBMCs be likely to alleviate the restrictions imposed by APOBEC3G & Tetherin?

   If so, perhaps the XMRV that WPI claims to find in CFS PBMCs is actually coming from other cells and merely ‘contaminates’ their PBMC preps. If other labs’ PBMC preps were cleaner, that could help explain some of the discrepancies.

3. #3 gf1

   March 5, 2010

   I just came upon this patient write up of an XMRV presentation, which seemed relevent. It mentions that XMRV does seem to be surprisingly difficult to detect by PCR, and also that contamination of cell lines seems common too.

   “Dr. Yasuhiro Ikeda Assistant Professor, Dept. of Biochemistry & Molecular Biology, Mayo Clinic
   Characterization of a novel human retrovirus Characterization of a novel human retrovirus XMRV: Prevalence, antiviral drug sensitivity, and small animal model development
   UCDMC Cancer Center auditorium, 4501 “X” Street, Sacramento Thursday, March 4, 2010, 9:00 a.m. – 10:00 a.m.

   Disclaimer, the information Dr. Ikeda presented is not formally published. After his talk, I asked him to e-mail me what he would of the research information available from his lecture or otherwise. He seemed agreeable. I sat in the first row but my audio recording turned out very poor, and he has an accent. I have to get a different cable to download the audio file to my computer. I have a science background, but it’s not in virology. This is only my interpretation of what he presented from notes, recollection and my poor recording.

   Dr. Ikeda was impressive, friendly, and seemed meticulous. He presented research involving XMRV detection by PCR and antibody, cancer, antivirals, and finding a mouse model to grow the XMRV virus. The lecture was an hour long so he moved fast.

   He started with an overview of prostate and ME/CFS XMRV research, positive and negative associations. He presented the XMRV association with ME/CFS studies matter of factly as 1 for and 3 against with DeRisi skeptical.

   There was a slide about an indirect association of XMRV with H pylori, and Hepatitis C. He didn’t go into detail.

   The cell receptor for XMRV is XPR1.

   After testing many types of mice they infected Mus pahari (wild-derived) mice with XMRV and thought them suitable (but they like to play dead and bite). They discovered one California strain of mouse that harbored an endogenous retrovirus closely related to XMRV sequences. The XMRV they sequenced had very few mutations. They found the virus in their infected mice most often in the spleen, blood and brain, not prostate. They were curious about the leukemia connection because they found very few infected leukocytes.

   A number of antiviral drugs were tested at different concentrations with XMRV infected cells. They thought AZT seemed to be the only one that worked well without excessive toxicity to the cells (with about 100X reduction in viral activity). He stated that after stopping AZT treatment of the cells the virus started to replicate at rates comparable to before treatment. They had a slide that showed a sequence where HIV and XMRV were similar, and that they thought the drug was interrupting the replication at those sequences.

   They did a human prostate cancer study. 159 samples of prostate cancer tissue (grade 5-7), and 201 controls were tested for XMRV. 4.5% were XMRV positive in PC tissue. 2.5% were XMRV positive in prostate tissue controls .

   There was some confusing data on XMRV detection. He reported PCR seemed to be much less sensitive and often didn’t detect XMRV (and they used multiple PCR testing with some samples to find XMRV) than with other methods. They found real time PCR was more sensitive than nested PCR. They didn’t find XMRV in some of their first pass testing using western blot. They said that the positive tests had weak signals.

   They are looking at XMRV surface glycoproteins for targeting. I’m not sure if he was talking vaccines or other treatments.

   I found this very interesting. They found some standard cell lines of LnCap and 22Rv1 (biosafety level 2 lines) were already infected with XMRV before they came to their lab. Not all, just from some of their sources so they think that labs should be screening received cell lines by real time PCR.

   At the end there was about a 10 minute presentation about stem cell research in his lab. He talked about adult stem cells and differentiating them into specific cell functions; heart, nerve, and so forth. He didn’t say if this was related to his XMRV research.

   In our discussion after his presentation he stated he is only consulting with Silverman. They will probably not so ME/CFS research because Mayo isn’t big into ME/CFS. The docs there think the patient population is too heterogenous. I said the Science study used the most restrictive patient criteria and others the least restrictive. My impression was that he didn’t know the details of the different definitions. “

4. #4 ragarth

   March 6, 2010

   Dr… Bishop?

   By any chance is he working with the FBI to save us from destruction with a parallel universe that he created?

5. #5 KevinS

   March 6, 2010

   I think these findings on restriction are exactly in line with what we are seeing in patients who are positive for the virus. Since XMRV is a gamma retrovirus it needs dividing cells (rapidly dividing is better) to infect. Cancer patients obviously have rapidly diving cells, and some CFS patients have markers of chronic immune activation so lots of lymphoproliferation.

   The study shows XMRV has the tools to use the receptor on most cells. It looks like TRIMs do not touch the virus. This means there is no stopping this virus from integrating. Since it integrated into a cell that is proliferating the virus gets copied as a pro-virus. This is especially true if the virus integrated into an area of the genome where it does not get copied well.

   Once the virus is in it has trouble getting out and infecting other cells since APOBEC and Tetherin put the breaks on other rounds of infection.

   If the virus is being shed from a mouse with an endogenous virus in its genome, there would be very little sequence diversity of the virus that is being shed. If the virus can infect cells but not get out very well, then the provirus we see has been copied by accurate polymerases. This explains the apparent lack of sequence diversity. We don’t see viral sequences that look like they encountered APOBEC because the virus is not really replicating very well. This is why it may be hard to detect it. You need to find the cell or subset of cells with the provirus among trillions of cells. We have found the virus in dividing cell types that are easy to access, cancer and blood. It would be likely that we would see it in other dividing cell types that are less accessible.

   This is all wild speculation, but in my head it makes sense.

6. #6 sardine

   March 8, 2010

   I know this is off topic, but I read this site to try to get a handle on some biology, of which I am sorely ignorant (MechE,) but when you see some of these bacteria speciate in the lab (and other observed forms of speciation) are there changes in the DNA? And is there any basic articles I could read on the subject.
   I have spent some time searching but haven’t found anything that I could understand.

   Thanks in advance for any help you all could give me on this,

   Dale

7. #7 GK

   March 16, 2010

   Hi, erv-Germany-is-not-part-of-Europe-because-there’s-no-XMRV-in-Europe-although-it-was-found-in-Germany-in-2008.

   See if you’re capable of being an objective scientist again when it comes to XMRV….

   THE PREVALENCE OF XENOTROPIC MURINE LEUKEMIA VIRUS-RELATED VIRUS IN
   HEALTHY BLOOD DONORS IN JAPAN

   Rika A. Furuta1, Takayuki Miyazawa2, Takeki Sugiyama3, Takafumi
   Kimura1, Fumiya Hirayama1, Yoshihiko Tani1 and Hirotoshi Shibata1

   1 Department of Research, Japanese Red Cross Osaka Blood Center, 2
   Laboratory for Viral pathogenesis, Institute for Virus Research, Kyoto
   University, 3 Department of Urology, Nishiwaki Municipal Hospital.

   To estimate the impacts of infection with xenotropic murine leukemia
   virus-related virus (XMRV) on the blood service, we investigated the
   prevalence of this virus in both prostate cancer patients and healthy
   blood donors in Japan. All specimens from the prostate cancer patients
   were collected after obtaining their written informed consent. The
   ethical committee of the Japanese Red Cross Society approved the
   examination of XMRV antibodies, but not nucleic acids, in random donor
   sera.

   All serum samples of healthy blood donors tested negative for HIV-1,
   HIV-2, HTLV-1, hepatitis B virus, hepatitis C virus and human
   parvovirus B19.

   To make a recombinant virus as test antigens for the antibody
   screening, 293T cells were transfected with an expression vector
   carrying an XMRV provirus clone, namely, VP62 (kindly gifted by Dr. R.
   H. Silverman). We used an env-defective mutant of HIV-1 derived from
   pNL4-3 (kindly gifted by Dr. A. Adachi) as a negative control.

   Two days after transfection, the culture supernatants of the
   transfected cells were collected and concentrated 20 times by
   centrifugation. We implemented western blotting assay to screen
   antibodies against XMRV in sera because a high background was observed
   if we performed enzyme-linked immunosorbent assay. In the western
   blotting, the blot strips were incubated with the serum samples
   diluted 1:100 with 5 % skim milk in Tris-buffered saline overnight at
   4°C.

   Two of 32 serum samples collected from the prostate cancer patients
   and 5 of 300 serum samples collected from healthy blood donors tested
   positive for antibodies against XMRV Gag protein. We did not observe
   any specific signals against Env proteins in the western blotting. Of
   the 2 serum samples that were obtained from prostate cancer patient
   and tested positive for anti-XMRV antibodies, the XMRV specific
   nucleic acid sequence was detected in only one sample (patient #24) by
   using nested RT-PCR.

   In addition, we collected 7 mL of whole blood cells from the patient
   #24 and cultured the peripheral blood mononuclear cells (PBMCs) in the
   presence of recombinant interleukin 2 and concanavalin A.

   The PBMCs were harvested after 10 days of culture, the virus was
   isolated from the cells by performing a LacZ marker rescue assay and
   RNA and genomic DNA were extracted. The nested PCR performed to detect
   XMRV yielded positive results for both genomic and RT PCR, although
   the virus was successfully isolated in only 1 of 3 independent
   experiments. To examine the susceptibility of PBMCs derived from
   healthy individuals to XMRV, we inoculated activated PBMCs from 3
   healthy volunteers with the culture supernatant of the PBMCs obtained
   from patient #24. By using the nested PCR, we detected the
   XMRV-specific nucleic acid sequence in the genomic DNA of the PBMCs
   obtained from 2 of the 3 healthy volunteers.

   We conclude that XMRV infection is prevalent among both prostate
   cancer patients and healthy individuals in Japan. Although our study
   had a limited sample size, the prevalence among blood donors as
   determined by identifying XMRV-specific antibodies was found to be
   1.7%, while that among prostate cancer patients was found to be 6.3%
   (P<0.05, one-sided Mann-Whitney U-test).

   The results of genomic PCR performing on the PBMCs indicate that XMRV
   is sustained in a few fractions of blood cells and can spread through
   blood even though the virus replication rate appears to be very low.

   Source: 1 Department of Research, Japanese Red Cross Osaka Blood Center, 2
   Laboratory for Viral pathogenesis, Institute for Virus Research, Kyoto
   University, 3 Department of Urology, Nishiwaki Municipal Hospital.

8. #8 ERV

   March 16, 2010

   Artard– OMFG THEY FOUND XMRV IN 8 PATIENTS IN GERMANY AND THEN NO ONE COULD REPLICATE THEIR FINDINGS!!! WARBLEGARBLE!

   Also, I already wrote about the Japanese test.

   Thanks for yet another insightful comment.

   Yours in Christ,
   Abbie

9. #9 ERV

   March 16, 2010

   Artard– So just to be 100% clear, here: A grown, professional scientist accusing researchers who dont agree with her of scientific fraud, making up data, scamming to get published, and accepting bribes from Big Pharma/Big Insurance/whatever, with no evidence to support those assertions is absolutely fine with you.

   But calling this ‘professional scientist’ a cunt if she cannot provide evidence for her claims is ‘wrong’.

   You are a fucking moron.

10. #10 GK

    March 18, 2010

    Touche!

    Stay classy, darlin’.

11. #11 sue

    April 8, 2010

    so which cells have the TRIM5alpha thingie?

12. #12 sue

    April 8, 2010

    it says most cells in primates have it….so i guess the thought of eradication of XMRV once established is a lost cause :-/

13. #13 Dan

    April 10, 2010

    Let’s see Judy Mikovits PhD with 20 years of experience with the National Cancer Institute knows less…than…uh a student who doesn’t even have a graduate degree. Another ego manic vying for attention or do you work for UNUM?

14. #14 BurntOffering

    August 27, 2010

    “I found this very interesting. They found some standard cell lines of LnCap and 22Rv1 (biosafety level 2 lines) were already infected with XMRV before they came to their lab. Not all, just from some of their sources so they think that labs should be screening received cell lines by real time PCR.”

    I hope that WPI/VIPDX has been running sufficient controls on pre-culture LnCap samples. This seems a plausible explanation for the disparate findings. If WPIs findings collapse under the weight of contamination, it will go badly for them. Their work is needed but they have surely alienated a lot of scientists.