Mystery Rays from Outer Space

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

October 31st, 2009
October 30th, 2009

Eradicating malaria?

Of the tools that are available or envisioned, only a highly efficacious, long-lasting vaccine would provide the degree and duration of transmission-blocking needed to achieve the simultaneous protection applied across a whole population at contiguous risk that is required to reduce and maintain R0 < 1 for that entire area

Plowe, C., Alonso, P., & Hoffman, S. (2009). The Potential Role of Vaccines in the Elimination of Falciparum Malaria and the Eventual Eradication of Malaria The Journal of Infectious Diseases DOI: 10.1086/646613


… taking Bill and Melinda Gates’ challenge to heart and considering it seriously, we have come to the conclusion that eradication just might be possible, but only if a new set of tools are developed that focus on reducing the effectiveness of the mosquito vector. … Could a vaccine alone eradicate malaria? … A vaccine used in combination with antimalaria drugs and vector control could be quite effective in reducing the disease burden. However, eradication is a different story. We would argue that, in addition to vaccines, antimalarial drugs, and presently available vector control methods, eradication will require special tools that we have yet to develop.

Miller, L., & Pierce, S. (2009). Perspective on Malaria Eradication: Is Eradication Possible without Modifying the Mosquito? The Journal of Infectious Diseases DOI: 10.1086/646612

Further reading
Malaria eradication: The smallpox precedent
Malaria vaccination – a victim of its own (feeble) success
Malaria eradication?
October 28th, 2009

On designing malaria vaccines

Our deepening knowledge of the immune evasion mechanisms of malaria is revealing the parasite’s ability to orchestrate the human immune response. … It would thus seem futile to test novel antigens or vaccine platforms without first incorporating features designed to circumvent parasite immune evasion strategies. … The prominent feature of a successful vaccine targeting chronic infectious agents such as malaria may therefore not be the antigens it includes, but rather the strategy used to free the immune system from its shackles.

Casares, S., & Richie, T. (2009). Immune evasion by malaria parasites: a challenge for vaccine development Current Opinion in Immunology, 21 (3), 321-330 DOI: 10.1016/j.coi.2009.05.015

October 23rd, 2009

On evolution of immunity

[W]e have estimated that natural selection drives twice as much change in immune-related proteins as in proteins with no immune function. Interestingly, the rate of adaptation is also more variable among immunity genes than among other genes in the genome, with a small subset of immunity genes evolving under intense natural selection. We suggest that these genes may represent hotspots of host–parasite coevolution within the genome.

Obbard, D., Welch, J., Kim, K., & Jiggins, F. (2009). Quantifying Adaptive Evolution in the Drosophila Immune System PLoS Genetics, 5 (10) DOI: 10.1371/journal.pgen.1000698

(This is particularly interesting to me because I’m trying to look at co-evolution between pathogens and immunity myself.  I’ve been tentatively suggesting that adaptive immune components (co)-evolve faster than innate immune components; of course, Drosophila only have innate immunity, so this paper suggests that the innate immune system also evolves rapidly.  That’s not unexpected, and doesn’t disprove my hypothesis, but it’s interesting anyway.  Also, there are some techniques in here I might be able to make use of.)

October 19th, 2009

Brainwashed killers

TRegs in normal skin
TRegs in normal skin

Tumors are supposed to be destroyed by our immune system. So how come we still see tumors?

A big part of the answer is probably that our immune system is very good at destroying proto-tumors, but is not so good at handling those that manage to sneak through and grow to the point of detectability. That splits the first question into two questions: Why do some proto-tumors manage to sneak through, not being eliminated by the immune system? And why is it that detectable tumors are not effectively handled?

The first part, I think, may often be related to cell-intrinsic immune escape mutations. That is, pre-cancerous cells are constantly being attacked by the immune system; in turn (if they survive long enough) they constantly mutate, doing things like damaging the antigen-presentation pathway that makes them recognizable by the immune system. Eventually, they find some configuration that reduces the rate at which they’re killed. Once cancer cell replication is even fractionally greater than destruction,1 a tumor can begin to grow.

So that’s probably the earliest stage of tumor growth. But once tumors reach a certain size, a second factor kicks in. Chronic immune responses are dangerous; after all, the whole point of the immune system is to kill things. The chronic immune response against the growing tumor is now shut down. This has been understood for quite a while — the immune system often becomes “tolerant” of a tumor. More recently, it’s become clear that it’s not merely “tolerance” (which implies that the immune system is simply benignly ignoring the tumor); the presence of a tumor actively forces the immune system to shut itself down, slamming on the brakes rather than just peacefully coasting by.

Brakes are a fundamental part of an active immune response. If you look at diagrams of normal immune responses, they show inverted “U” shaped curves (in here and here, for example), where the response is triggered, rapidly ramps up, hopefully does its thing, and then just as rapidly shuts down to near-background levels once again. There used to be a sort of general feeling that this was a rather passive thing — pathogen stimulates response, response destroys pathogen, no more stimulus, response goes away — but now we understand that the shut-down phase is just as active and dynamic as the upward curve. Just as with the upward phase, there are all kinds of different mechanisms to control the response; one of the most important is the “Regulatory T cell” (TReg).  And it’s pretty clear that TRegs are involved in controlling the immune response to tumors (I talked about that here, and links therein).

TRegs have been known for a while (I gave a brief history, including the I-J fiasco, here). The usual description of a TReg includes a number of markers;2 one of the most basic is CD4. CD4 T cells used to be lumped together as “T Helper” cells, but now we have multiple sub-specialties in the CD4 category, and TRegs are one of those specialities.

More recently, TRegs — or at least cells that function the same way as TRegs — have been described in the CD8 population of T cells.3 CD8 T cells are traditionally called “Cytotoxic T lymphocytes” (CTL) (although it’s been increasingly clear that cytotoxicity is just one of many functions a CD8 T cell can offer), but it seems that these variants of CD8s can actively shut down an ongoing immune response, in a specific and targeted way. There seems to be a trend to calling these cells “suppressor cells” rather than “TRegs”. “Suppressor T cells” is an older term that was out of favor for a while, but it’s probably useful to bring it back and distinguish between the natural TRegs and some of the other cells that can do something similar but that have different sources and origins.

At least some of the CD8 suppressor T cells can arise from apparently-conventional CD8 T cells. That is, you can pull CD8 T cells out of a normal mouse’s spleen, and depending on what those cells see and are exposed to, they could progress to being conventional CTL — killing tumor cells, producing interferon and other cytokines, generally being a destructive force — or they could become suppressor CD8 T cells, and actively prevent that destruction from happening.

Brainwashed killerIt turns out that one of the forces that can drive a CD8 T cell into being a suppressor T cell is a tumor. A recent paper from Arthur Hurwitz’s lab4 shows this quite clearly. They had shown previously that transferring specific CD8 T cells into a tumor-bearing mouse resulted in what they called “tolerance”.5 But now they demonstrate that it’s more than that; the transferred CD8s are converted into suppressor T cells that actively shut down immune responses.

Tumor-infiltrating TcR-I cells suppressed the in vitro proliferation of both melanoma Ag-specific CD8+ (37B7) T cells and OVA-specific CD4+ (OT-II) T cells. … Even at a ratio of one TcR-I cell to four responder T cells, we observed 30% suppression of proliferation. 4

This isn’t the only way that tumors escape immune recognition, but (at least for some tumors) it may be an important one. It’s clearly an important consideration for things like tumor vaccines and immune therapy, because it suggests that immunizing with tumor antigens (and thereby generating lots of tumor-specific CD8 T cells) may actually increase the suppressive effect of the tumor.

The conversion of CD8+ effector T cells into suppressor cells may be one mechanism by which tumors restrict the immune response from effectively controlling tumor growth. As subsequent effectors infiltrate the tumor, either following peripheral sensitization or as a result of adoptive transfer therapy, the induced regulatory cells may suppress these new effectors and reduce their ability to confer tumor immunity. This cyclic suppressive process may contribute to the profound loss of antitumor responses following adoptive immunotherapy. 4

(My emphasis.) On the other hand, if this is a common mechanism, then overriding it — which should be possible, using cytokines, specific T cell subsets, and/or targeted receptor ligands — may switch the suppressive population abruptly back into an effector group, turning the brainwashed traitors into resistance fighters.

  1. Destruction would include far more than immune destruction, of course — it would include cells that become differentiated and no longer replicated, cells that outgrow their oxygen supply, cells that undergo apoptosis, and so on[]
  2. FoxP3, CD25, and so on[]
  3. I’m not sure who made the first identification; this looks as if it’s one of those fields where there were incremental advances, hinting more and more strongly at the presence of these cells, but with no single clearcut starting point. Papers in the early 2000s start to point at regulatory CD8s, and by 2004 a handful of relatively high-profile papers fairly solidly identified them. A 2004 review paper is
    Zimring, J., & Kapp, J. (2004). Identification and Characterization of CD8+ Suppressor T Cells Immunologic Research, 29 (1-3), 303-312 DOI: 10.1385/IR:29:1-3:303[]
  4. Shafer-Weaver, K., Anderson, M., Stagliano, K., Malyguine, A., Greenberg, N., & Hurwitz, A. (2009). Cutting Edge: Tumor-Specific CD8+ T Cells Infiltrating Prostatic Tumors Are Induced to Become Suppressor Cells The Journal of Immunology, 183 (8), 4848-4852 DOI: 10.4049/jimmunol.0900848[][][]
  5. Anderson MJ, Shafer-Weaver K, Greenberg NM, & Hurwitz AA (2007). Tolerization of tumor-specific T cells despite efficient initial priming in a primary murine model of prostate cancer. Journal of immunology (Baltimore, Md. : 1950), 178 (3), 1268-76 PMID: 17237372[]
October 13th, 2009

Lab escapees

Influenza virion
Influenza virion

At this point in 2009, I think most people probably have a general grasp of influenza virus infection patterns.  At the simplest level, a few strains of virus circulate every year, with relatively small changes year-to-year.  Every so often, a new strain, with larger changes, appears and spreads globally, often becoming the dominant “base” strain for a while (that is, circulating annually with smallish changes each year) until it in turn is replaced by a new strain.

A particularly interesting “new” influenza strain appeared in 1977.  At that time the dominant circulating strains didn’t include any H1N1 strains; H1N1 had gone extinct in humans around 1957. (H1N1 was still circulating in swine, though.) An H3N2 strain, the tail end of the 1968 pandemic influenza, was the major strain. 1 But in 1977, H1N1 returned, first isolated in China and subsequently in Russia, then rapidly spreading throughout the world and remaining endemic since then, circulating in parallel with H3N2 strains since then.  (That’s why influenza vaccines are trivalent — they cover both an H1N1 and an H3N2 strain of influenza A, plus an influenza B strain.)

It was quickly discovered that the “new” H1N1 was not new at all.  Even without modern genomic sequencing systems, Peter Palese’s group was able to show that the 1977 H1N1 was actually an old strain,2 described in 1950, that had re-appeared without any evidence of evolution throughout the dozen intervening years. Although Palese didn’t outright say it at the time, this almost certainly was a laboratory strain of influenza that had escaped back into the wild.

Finally, it is possible that a 1950 influenza virus was truly frozen in nature or elsewhere and that such a strain was only recently reintroduced into man. 2

(My emphasis.)

Influenza signA couple of side notes before I continue.  There are several other claims in the literature that various influenzas since 1977 are lab escapees.  Most, if not all, of those claims are almost certainly wrong, and represent a different kind of lab contamination — reference strains of influenza that have contaminated the test strain, within the lab, rather than a lab strain actually circulating in the wild. 3 This form of lab contamination with reference strains seems to be a relatively common source of error,4 and it’s certainly a problem, but isn’t an actual direct threat to the population.

In particular, the swine-origin H1N1 is not a lab escapee (and, in spite of the rumors among bloggers who don’t know anything about viruses, but who dearly love a conspiracy theory, it’s not an artificial construct).  Although the details of the SOIV origins are fuzzy, its parents and family tree is pretty clear by now.

That said, lab escapes are not unheard of.  Notoriously, the last case of smallpox was a lab escape, and the 2007 outbreak of foot and mouth disease in the UK was almost certainly an escaped lab strain from the Pirbright Research Center. 5 The problem with the conspiracy theories6 isn’t that virologists say lab escape is impossible.  We know perfectly well that lab escapes can, and do, happen.  The reason the conspiracy theories are wrong is that escapes have happened and been promptly detected and reported.  There’s no conspiracy.

Dengue virus
Dengue virus

What may be the latest example of this was just reported in PLoS One.7  In the course of analyzing Dengue virus strains circulating in Brazil and Columbia, an unexpected strain was detected: It is a strain that was present in Asia some 20 years ago, almost unchanged since.  Like influenza, dengue viruses mutate and evolve fairly rapidly; this kind of stability (35-fold lower than expected) would be extraordinary in a virus that’s been circulating for two decades.  What’s more, these viruses don’t show geographic clustering. Normally, dengue viruses circulate locally and develop local sub-strains; this older virus, though, is very similar in Brazil and Columbia, and doesn’t group with local viruses:

DENV-3, when introduced to a new area, evolves locally, resulting in geographically-associated clusters closely related to other virus recently circulating in other region.  Interestingly, we have shown in this study that viruses recently circulating in Brazil and Colombia form a monophyletic cluster together with viruses isolated in Asia more than two decades ago.7

There are two obvious possible explanations.  One is that this represents lab error — the strains they were analyzing were somehow contaminated with this older strain.  The other is that this is a lab escapee:

Could some how this strain escape from the laboratory and started to infect humans, thus explain the close relationship of the new viruses with genotype V strains?7

I’d like to see this work repeated by an independent lab to make sure it’s not lab contamination (and the authors clearly want the same thing: “Therefore, more studies are needed to confirm the origin of American genotype V viruses”) but it certainly seems like a plausible explanation.

I’m not a Dengue expert by any means, but I don’t think there’s anything especially hazardous about the “new” (old) strain — Dengue is already widely present in these areas, and I don’t think having one more strain in circulation adds to the general population risk.  But I’d like to see an expert’s opinion on this; interactions between Dengue strains are important in the disease.

In any case, it reinforces (if reinforcement was necessary) the importance of proper lab procedures and security.

  1. A nice review is Morens, D., Taubenberger, J., & Fauci, A. (2009). The Persistent Legacy of the 1918 Influenza Virus New England Journal of Medicine, 361 (3), 225-229 DOI: 10.1056/NEJMp0904819[]
  2. Recent human influenza A (H1N1) viruses are closely related genetically to strains isolated in 1950.
    Nakajima K, Desselberger U, Palese P.
    Nature. 1978 Jul 27;274(5669):334-9.[][]
  3. Worobey, M. (2008). Phylogenetic Evidence against Evolutionary Stasis and Natural Abiotic Reservoirs of Influenza A Virus Journal of Virology, 82 (7), 3769-3774 DOI: 10.1128/JVI.02207-07[]
  4. I’ve previously cited
    Krasnitz, M., Levine, A., & Rabadan, R. (2008). Anomalies in the Influenza Virus Genome Database: New Biology or Laboratory Errors? Journal of Virology, 82 (17), 8947-8950 DOI: 10.1128/JVI.00101-08
    and see also

    Li, J., Dohna, H., Miller, J., Cardona, C., & Carpenter, T. (2009). Identifying errors in avian influenza virus gene sequences and implications for data usage of public databases Genomics DOI: 10.1016/j.ygeno.2009.09.005 []

  5. Cottam, E.M., Wadsworth, J., Shaw, A.E., Rowlands, R.J., Goatley, L., Maan, S., Maan, N.S., Mertens, P.P., Ebert, K., Li, Y., Ryan, E.D., Juleff, N., Ferris, N.P., Wilesmith, J.W., Haydon, D.T., King, D.P., Paton, D.J., Knowles, N.J. (2008). Transmission Pathways of Foot-and-Mouth Disease Virus in the United Kingdom in 2007. PLoS Pathogens, 4(4), e1000050. DOI: 10.1371/journal.ppat.1000050[]
  6. Apart from the fact that most of them are batshit crazy[]
  7. Aquino, V., Amarilla, A., Alfonso, H., Batista, W., & Figueiredo, L. (2009). New Genotype of Dengue Type 3 Virus Circulating in Brazil and Colombia Showed a Close Relationship to Old Asian Viruses PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007299[][][]