XMRV is so hot right now.
Read the paper on XMRV and Chronic Fatigue Syndrome last weekend:
My conclusions from the paper: XMRV is capable of infecting humans and producing viable progeny.
How this fact relates to CFS, Im still not sure.
Let me go through exactly what these researchers did.
1– Nested PCR looking for XMRV genomes.
Nested PCR is kinda ‘better’ than regular PCR, especially when we are talking about retroviruses. How do you know the signal you are seeing is because of XMRV, and not, say, an endogenous retrovirus that your primers happen to bind to? With nested PCR, you say ‘Hey, some of this signal might be non-specific in our first round of PCR, but with this second round, we know the resulting signal going to be what we are looking for, and its going to be a nice bright band.
My conclusion: There is XMRV DNA in the white blood cells of some patients with CFS. Patients who were positive for gag were also positive for env, except for one ‘Normal’ patient who was pos for gag only.
There was nothing particularly ominous about this data. Not sure I would have done it any differently, except Id probably use real-time PCR instead of just running out gels.
2– Looking for full-length XMRV RNA genomes, phylogeny
The sequences of XMRV isolated from CFS and prostate cancer patients clusters together in a phylogenetic tree. They do not cluster with other, similar viruses in mice.
My conclusion: This tree looks like trees I generate every day looking for relatedness between mother/child samples vs HIV-1 consensus sequences and SIV variants. Nothing ominous about this data either. They didnt contaminate their shit.
3– Flow Cytometry looking for XMRV proteins in white blood cells
Just because cells have XMRV DNA doesnt mean they make any XMRV proteins. Sometimes with xenotropic infections, we are like the cockroach hotel– viruses can check in, but they cant check out.
So they used antibodies to MLV/SFFV (just another control) to see if the white blood cells from CFS patients were making MLV-like proteins. They were. Normal controls didnt.
My conclusions: Pretty damn weak shifts in mean fluorescence intensities, but they were shifts, while the cells from ‘normal’ humans didnt shift. *shrug*
4– Western Blots looking for XMRV proteins in white blood cells
This is just another way of confirming that DNA positive cells were actually making proteins. Blow up some white blood cells, run their guts out in a gel, and look for the proteins with antibodies.
My conclusions: Whoooooeee them be some ugly, over exposed, wrong side of the film Western Blots! Seeing them in ‘Science’ really does make me feel better about my lab hands, and a little annoyed at my perfectionism, but their CFS samples are positive, and ‘normal’ ones arent. *shrug*
5– Which white blood cells are infected?
Okay, I only want one thing from the bags of blood I get from the blood bank– CD4+ T-cells. Use em to play with HIV-1. The trick is purifying the CD4+ T-cells from all the other crap in your blood. Soooooo first thing you do is spin a tube of blood real slow over this sugar/salt solution and you pellet red blood cells, plasma floats, and your white blood cells form this creepy cloud between the other two layers.
This white layer still contains B-cells, CD4+ T-cells, CD8+ T-cells, macrophages, etc, so then you have to use this nifty technique to purify B-cells only, or CD4+ T-cells only, etc.
Once these folks got purified populations of cells from CFS/’normal’ patients, they looked for XMRV proteins via flow. Both B and T-cells were positive in CFS patients.
My conclusions: Once again, weak shifts in fluorescence, but they were shifts. However, now I am having some ‘issues’. MLV is a simple retrovirus, whether its in mice or humans. It requires actively dividing cells to infect. Thus it is not infecting mature T-cells (like HIV-1 does), it must be infecting these cells at a very early stage in their development, ie, how MLV infects mice– bone marrow. Thats why we use it for hematopoietic stem cell gene transfer.
Yet humans dont get cancer from all of this XMLV insertional mutagenesis in CFS patients, even though the kids in our tightly controlled defective moloney murine leukemia virus gene therapy study got leukemia. What?? *FROWNY FACE*
6– Western Blots to assess whether the detected XMRV proteins actually make infectious virus
Co-culture of white blood cells from CFS patients and a susceptible cell line lead to infection of the cell line (cell-cell transmission that retroviruses sometimes prefer).
Supernatant from cultured white blood cells from CFS patients could infect the susceptible cell line (cell-free virus).
Images of the susceptible cell line showed budding viruses.
My conclusions: This is not the normal way of showing your viruses are infectious. The normal way is an assay that measures increases in reverse transcriptase activity over time. I wouldnt have done this experiment this way.
7– Detection of XMRV antibodies in patients
Instead of using patient white blood cells and known antibodies to do flow, they flipped it around and used a cell line they knew expressed XMRV, and used antibodies from patients. If the cells didnt light up, the patients dont have antibodies to XMRV. Some of the CFS patients had XMRV antibodies.
My conclusion: Nice study design. These folks arent amateurs.
The science of this paper is fine. Their experiments are fine. And, there is clearly a bias for the presence of XMLV in CFS patients.
BUT, this story doesnt make sense.
Not all the CFS patients have XMLV. I assure you that all AIDS patients have HIV-1.
XMLV in nature gives you CFS. ‘XMLV’ infection in gene therapy trials gives you leukemia.
You know, this paper, while fine, highlights for me One Of The Things Wrong With Research. Instead of doing some basic goddamn virology, cell biology, and biochemistry, we jump up with “OMFG CFS IS CAUSED BY A RETROVIRUS OMFG SCIENCE XPRESS! XPREEEEEEEEEESSSSS!!”
Its the same damn shit hole we have ourselves in with HIV-1. “VACCINES! VAAAAAAAACIIIIINES!… oh wait, maybe we should have done some basic virology before we started throwing shit in vaccines we now know wont work after we did some basic virology.” Oh, but determining receptors and cell tropism of viruses, even though knowing that information is fantastic for determining future directions/future questions/future studies, isnt gonna get you a ‘SCIENCE XPREEEEEEEEEEEESS!’ paper. Its not sexy. Basic population dynamics of a virus? Not sexy, even though it is essential information for logically designing a vaccine.
The most valuable piece of info I got from this paper and the marketing of this paper, is how much I am really, really, really starting to hate ‘Science Xpress’.
Its a slut.