Mystery Rays from Outer Space

Meddling with things mankind is not meant to understand. Also, pictures of my kids

September 7th, 2008

Viruses, fitness, and unfitness

Hepatitis C virus (HCV)It’s become pretty clear that one way HIV persists in spite of an active, powerful immune response is to mutate its immune targets: “immune escape”.  HIV isn’t the only virus that does this, and we can learn from the others.

Cytotoxic T lymphocytes (CTL) identify virus-infected cells by recognizing short peptides, usually about 9 amino acids long. Each CTL is fairly specific; it only recognizes a single sequence. That means that if even one of the nine amino acids in its target mutates, the CTL is blind to the virus. If the CTL response to a virus is limited to a single peptide (which is, to a first approximation, the most common situation) then this single mutation will allow the virus to escape from the immune system, at least until new CTL arise targeting some different peptide.

The downside of this, from the virus’s viewpoint, is that it doesn’t really “want” to mutate itself. There are a limited number of sequences which allow the virus to replicate and spread efficiently, and to the extent that the mutations drive the virus away from these fairly optimal sequences, the virus is less “fit”. That means that the immune response can actually limit the virus’s replication even after (in fact, because) the virus has mutated away from CTL recognition.

What are the conditions under which this sort of continual partial control and constant escape can take place? One fairly obvious point is that the virus must not be eliminated by the immune system. If the first (or even tenth) CTL response to arise gets rid of all the virus from the host, then there’s no more viral immune evasion. I pointed out a parallel instance of this earlier, where poliovirus undergoes mutation in a person, but only when the person has a deficient immune system and can’t completely clear the virus. The virus needs to undergo constant replication over a long period, which makes this less of an issue for things like herpesviruses — they’re long-standing infections, but typically establish a latent infection rather than replicating throughout the infection. It probably would be helpful for the virus to mutate relatively fast, as well — DNA viruses like adenoviruses (which possibly do continue replication in persistent infection) have a relatively low mutation rate compared to RNA viruses like poliovirus or retroviruses like HIV.

Hepatitis C posterImmune escape by hepatitis C virus

There are several lab animal and veterinary examples where something parallel to HIV immune evasion probably takes place (mouse hepatitis virus; perhaps feline infectious peritonitis virus), but the most popular choice for a close parallel to HIV is another human virus, hepatitis C virus (HCV). HCV, like HIV, can establish a chronic infection in immunocompetent people, and continually replicates. It’s been known that HCV mutates over time, and there’s decent evidence that much of this mutation is driven by escape from CTL. The parallels have become stronger with new evidence1 suggesting that virus fitness changes are an important factor in HCV immune evasion, as well, but there’s a twist that I, as least, haven’t seen in HIV.

In these experiments, the authors experimentally infected a chimpanzee with HCV (as with HIV, there are not many good animal models for HCV) and tracked the immune response, and the dominant viral genome sequences, over some seven years. What’s more, the authors then tested those mutant viruses for their ability to replicate, persist, and evade immunity.

As expected, HCV threw out a bunch of mutations, especially in the early stage of infection, and those mutants were not recognized by the immune system. On the other hand (also as predicted, from the work on HIV) these early mutants were not as good at replicating as was the original (immunogenic) virus: They were less fit.

HCV escape variants can be fit

But — and here’s the twist — there were at least three variants that evaded CTL, arising early (3 months, for one variant), or moderately late (10 months; two variants). The one that arose early was clearly less fit.  It didn’t replicate well even when there was no immune system controlling it (that is, in cultured cells in the incubator), and given the chance, it mutated back to the original sequence.

The later ones, though, were not obviously as damaged; they replicated pretty well in cultured cells, and they did not mutate back to the original parent sequence.

What’s more, one of these relatively-fit variants persisted, more or less unchanged, in the infected chimp for years after it arose. (The other variant, though “fit” in culture, was not in the host, because a new immune response arose that targeted that variant.)

So for HCV, CTL escape mutants can arise, and there is not necessarily a loss of fitness associated with the immune evasion. I don’t remember seeing this established with HIV, but it’s quite likely the same thing happens. (Perhaps it’s even been described in the literature and I’ve missed it.) When immune escape variants are fit and healthy viruses, the immune system hasn’t even imposed a fitness cost on the mutation, and the virus isn’t being significantly controlled by the immune response.

It would be nice to understand better where fitness costs arise, which immune responses drive viruses to these un-fit variants, and how to focus the immune response on a vulnerable target.


  1. Luke Uebelhoer, Jin-Hwan Han, Benoit Callendret, Guaniri Mateu, Naglaa H. Shoukry, Holly L. Hanson, Charles M. Rice, Christopher M. Walker, Arash Grakoui, Darius Moradpour (2008). Stable Cytotoxic T Cell Escape Mutation in Hepatitis C Virus Is Linked to Maintenance of Viral Fitness PLoS Pathogens, 4 (9) DOI: 10.1371/journal.ppat.1000143[]
September 4th, 2008

Tumors keep out T cells

No one is safe from cancer (ACS)We know a bunch of ways by which tumors avoid the immune system. Lots of tumors are defective in antigen presentation and natural killer cell recognition (that is, they should be poorly recognized by cytotoxic lymphocytes). These probably usually arise quite early in tumor development, before the tumor becomes detectable. By the time tumors are clinically apparent, there are often lots of regulatory T cells (TRegs, the cells that normally suppress immune responses that are directed against “self”) directed to the tumor, and those TRegs prevent anti-tumor immune responses from developing (see here for more on that).

If you’re trying to trigger an immune response to the tumor, you probably need to overcome both the defective T cell recognition of individual cells, and (especially) the suppressive TReg response that the whole tumor has induced. A new paper1 points out yet another problem that may need to be overcome before immunotherapy of tumors becomes generally useful.

One phenomenon that’s often associated with a better prognosis for tumors is the presence of T cells infiltrating the tumor (for example, see here and here). Presumably these infiltrating T cells are part of an immune attack on the tumor, and that’s causing the better prognosis (though it’s also possible that, say, the tumor is dying more rapidly for other reasons and that’s attracting T cells, but let’s not get distracted here). If so, cranking up the number of anti-tumor T cells and cranking up their activity by reducing the number of TRegs, should increase the number of infiltrating T cells and improve the prognosis. Jim Allison’s and Dan Littman’s groups show that’s not necessarily true.1

Tumor-infiltrating T cells and adhesion factors
Boosting adhesion molecule expression in tumor blood vessels
(red) allows more tumor-killing T cells (green) to gain access

A puzzling finding has been that getting rid of TRegs apparently does crank up the number of activity of circulating anti-tumor T cells, but does not have much clinical effect on the actual tumors. “Our data indicate that depletion of T reg cells after tumor establishment results in a dissociation between systemic immunity and objective clinical responses.1 Quezada et al. suggest that this is at least partly because even after getting rid of TRegs, T cells still have trouble getting in to tumors (that is, they remain circulating T cells, and don’t become infiltrating T cells), and this may be because the tumor blood supply is abnormal.

Several studies suggest that tumor vasculature may differ from regular vasculature upon tumor establishment, and that this altered vasculature is less permeable to tumor-reactive lymphocytes.1

The good news is that this may be a manageable problem, at least in some tumors; because radiation therapy seems to restore the tumor blood vessels to a more normal state, allowing better infiltration of anti-tumor T cells. ( If you’re expanding the number of anti-tumor T cells artificially, irradiation also helps the expanded T cells “take” in the patient, and may have other immunological benefits as well.) When Quezada et al. incorporated radiation into a rather complex series of immunostimulatory steps,  mice succeeded in rejecting established tumors.

Whether there is any clinical relevance to humans here still isn’t proven, but as far as I can see, all of the components of the treatment they used here have been used as anti-tumor therapy in humans — so it may be worth merging them and seeing if the end result is as encouraging as in mice.


  1. S. A. Quezada, K. S. Peggs, T. R. Simpson, Y. Shen, D. R. Littman, J. P. Allison (2008). Limited tumor infiltration by activated T effector cells restricts the therapeutic activity of regulatory T cell depletion against established melanoma Journal of Experimental Medicine, 205 (9), 2125-2138 DOI: 10.1084/jem.20080099[][][][]
September 1st, 2008

XPlasMap sneak preview

I develop XPlasMap on my Macbook Pro, which is running MacOS10.5.4, and so it’s kind of a pain making sure it will run properly on PowerPC machines and machines running OS10.4.  (I gave up supporting 10.3 a while ago, because that was even more work.)  We do have a PowerPC machine running 10.4, but I gave it to my wife and kids; so to get XPlasMap running universally I have to find a sliver of time when the PowerBook isn’t being used.  

I found an hour this morning and got all the modules1 and so on upgraded to the proper versions, and after another 15 minutes got XPlasMap running on the machine.  Unfortunately there seem to be a couple of bugs that are specific for either 10.4, or PowerPC (arrows can’t be dragged, for some reason) and before I could trouble-shoot, my wife kicked me off the machine.  (Does this happen to Steve Jobs?)

The good news, such as it is, is that XPlasMap seems to be working fine on my own machine.  So if you’re running OS10.5 on an Intel machine, and want to take a look at a new but beta and potentially buggy version of XPlasMap, try downloading version 0.99 from here.  Bug reports, comments, feature requests, complaints, suggestions, all gladly accepted.  Also, if it’s not immediately obvious how something works, let me know so I can make sure it’s documented.

This is a temporary link, so if you’re reading this in the future (say, after Sept 8/08) there’s no guarantee that there will be anything there.


  1. Upgraded Python to 2.5;
    wxPython to 2.8.8;
    BioPython to 1.4.7, I think it is;
    mxBaseTools to 3.something;
    installed Numeric, even though it’s out of date, because BioPython needs it;
    and installed ElementTree even though most of it is in Python2.5 because I need XMLWriter[]