Of course, this is exactly the reason I write Mystery Rays.

Anyway, as usual, I wrote out my little notes largely for the intrinsic benefits – it powerfully fixes things in memory, and forces me to formalize my thoughts the way I know I should (but don’t want to). A lot of notes I just file away, but it’s always nice to put them out there where they may be of some interest.

Oh, sure, it’s quite extraneous, and their very existence may not be 100% certain… I only mentioned it as an interesting whatever. A rare chance for me to add something interesting to your page (which I always read engrossedly)… I sure didn’t get very far with the MHC diversity/nondiversity enigma, despite much contemplation…

I wonder if these cell-penetrating Ig, assuming they are for real, will turn out to have any anti-infective relevence. I certainly haven’t heard of them doing anything except maybe contribute to lupus.

> For reasons that I don’t understand, even though there do seem to be reasonably constant regions on HIV they seem to be very poor inducers of antibodies, and the vast majority of the antibody response to the virus is to the variable regions. Teleologically, this makes sense (the virus would “want” to vary regions that are most immunogenic, and then having them variable it would be advantageous to make them more immunogenic) but I’m not sure mechanistically how that works.

Given that I’m not going very far into the mechanism, perhaps the following amounts to merely repeating what you have just said – and maybe you’ve dealt with this idea already in some of your immunodominance posts. (Perhaps, at least, the refs I’ll cite will be of interest, in any case.) But anyway here goes: how about “epitope competition” – the idea of immunodominance being a function not only of certain peptides loading well or poorly per se (and other things like that), but also being a function of competition between epitopes for immunodominance. The high immunogenicity of the variable domains may actually lower the immunogenicity of the constant domains. As these guys put it:

“Immunodominant epitopes are known to suppress a primary immune response to other antigenic determinants by a number of mechanisms. Many pathogens have used this strategy to subvert the immune response and may be a mechanism responsible for limited vaccine efficacies.”

I was confused for a minute about why they mentioned the “primary” immune response in particular. I think it’s to help contrast what they are talking about against the concept of original antigenic sin, since the latter concerns memory responses specifically. Anyway, it goes on…

“HIV-1 vaccine efficacy appears to be complicated similarly by a limited, immunodominant, isolate-restricted immune response generally directed toward determinants in the third variable domain (V3) of the major envelope glycoprotein, gp120. To overcome this problem, we have investigated an approach based on masking the V3 domain through addition of N-linked carbohydrate and reduction in net positive charge. N-linked modified gp120s were expressed by recombinant vaccinia virus and used to immunize guinea pigs by infection and protein boosting. This modification resulted in variable site-specific glycosylation and antigenic dampening, without loss of gp120/CD4 binding or virus neutralization. Most importantly, V3 epitope dampening shifted the dominant type-specific neutralizing Ab response away from V3 to an epitope in the first variable domain (V1) of gp120. Interestingly, in the presence of V3 dampening V1 changes from an immunodominant non- neutralizing epitope to a primary neutralizing epitope with broader neutralizing properties. In addition, Ab responses were also observed to conserved domains in C1 and C5.”

So at minimum, masking V3 redirected some Ig firepower against V1 – and possibly against some conserved domains as well, though the abstract above seems mildly ambiguous on that point and I don’t feel like reading the whole paper (namely, RR Garrity et al, “Refocusing neutralizing antibody response by targeted dampening of an immunodominant epitope”).

I wonder why they whipped out the N-linked carb masking tape, rather than just cloning the conserved domains alone, adding some adjuvant, and messing around with that.

Anyway it sounds like the variable domains may be significantly effective as a distraction display. But – and maybe I misunderstood you, and the following enigma was actually your whole point – how can a variable region remain hyper-immunogenic? Is the variation, perhaps, low and slow enough that the sequence can retain some agreement with binding motifs of host MHC alleles – or do whatever it is that it does to stay hyperimmunogenic? Not being a viro jock, I had to google for whatever might seem like an answer:

“A major goal of HIV and SIV research is to understand the selective forces driving variation in each of the variable domains of env. It is not the replication error rates that are remarkable for HIV and SIV, but rather the capacity of their envelope proteins to tolerate changes (Coffin 1986). Although rates of [envelope protein] sequence change can be reasonably measured over the course of years, the numbers are too high to permit extrapolation to an evolutionary timescale.”

http://books.google.com/books?id=Awcmfx8EaOAC&pg=PA603&lpg=PA603&dq=hiv+variable+domains+recombination&source=web&ots=MgWnodpcfo&sig=6MnZ9XBakZXFJr16utUORlb-s7Q

That was one of my thoughts; I thought I had seen something saying that transcytosing antibody went through the cytosol, but I was weaseling because I couldn’t remember for sure. Janeway says

When the poly-Ig receptor has bound a molecule of dimeric IgA, the complex is internalized and carried through the cytoplasm of the epithelial cell in a transport vesicle to its luminal surface. This process is called transcytosis.

So you’re right, it’s not free in the cytoplasm. (Fortunately, I don’t teach the antibody section of our immunology course.)

I also remembered reading about the cell-penetrating antibodies, but again I couldn’t remember details, and it was off topic enough I thought I could let it slide.

Your superinfection point is a good one, and I was thinking about commenting on the PLOS paper some time; it came as a surprise to me, because I had thought that previous studies had established that superinfection was rare or non-existent, implying that resistance could happen.

However, it doesn’t really change the feasibility of an antibody-based attack on invariant regions of the virus surface. For reasons that I don’t understand, even though there do seem to be reasonably constant regions on HIV they seem to be very poor inducers of antibodies, and the vast majority of the antibody response to the virus is to the variable regions. Teleologically, this makes sense (the virus would “want” to vary regions that are most immunogenic, and then having them variable it would be advantageous to make them more immunogenic ¹) but I’m not sure mechanistically how that works. It does mean that the constant regions get identified by screening large numbers of clones of monoclonals.

1. I think it would, anyway, but I’m not sure how much individual and how much population benefit are involved.

That’s a fascinating idea – and to me (though I’m not learned in vaccinology or HIV) it has that ring of something that really stands a chance of working out in practice. PLoS Pathogens recently had one on HIV superinfection; I read only the abstract:

“[S]tudies to determine the incidence of HIV-1 superinfection have yielded conflicting results. Furthermore, few studies have attempted to identify superinfection cases occurring more than a year after initial infection [...] Among 36 [infected, I think] individuals, we detected seven cases of superinfection, including cases in which both viruses belonged to the same HIV-1 subtype, subtype A. In five of these cases, the superinfecting strain was detected in only one of the two genome regions examined, suggesting that recombination frequently occurs following HIV-1 superinfection. In addition, we found that superinfection occurred throughout the course of the first infection: during acute infection in two cases, between 1–2 y after infection in three cases, and as late as 5 y after infection in two cases. Our results indicate that superinfection commonly occurs after the immune response against the initial infection has had time to develop and mature.”

http://pathogens.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.ppat.0030177

While I guess there is already pessimism in some or many quarters about prospect for a “traditional” HIV vaccine, I hadn’t heard that widespread superinfection was a possible phenomenon. Doesn’t seem to bode well for any “traditional,” well-precedented kind of vaccine.

> Yes, I know that some forms of antibody routinely penetrate cells as they’re pumped into the gut, for example, but let’s stay relevant.

I assume that trans-epithelial transcytosis of antibodies is solely endosomal (though I’ve had a hard time googling up a platinum ref on that, especially since I’m off-campus).

So, I am pretty sure that natural “cell-penetrating antibodies” as they’re called, which seem to access the cytosol and nucleus of the intact cell, are a separate phenomenon. I was shocked when I first learned about them, and thought they might bear mentioning despite being off-topic:

“An alternative hypothesis for the renal pathogenicity of anti-dsDNA antibodies was proposed more than 20 years ago, namely that certain autoantibodies could penetrate into living cells and thus induce damage. Work from several laboratories has recently provided firm support for this iconoclastic theory, which contradicted prevailing immunologic dogma that cell interiors are inaccessible to antibodies. Here, we review the evidence [...]”

Autoimmun Rev. 2004 Feb;3(2):7-11.
New approaches to the renal pathogenicity of anti-DNA antibodies in systemic lupus erythematosus.
Putterman C. PMID: 15003182

This subject isn’t a huge concern for me, so I’ve never plowed through the experimental papers to see what I think of said evidence. So far the idea seems not to have been fully baptized by the mightiest journals, though it has been mentioned briefly by Putterman (or perhaps it was Yaakov Naparstek) in the pages of the authoritative and excellent _Dubois’ Lupus Erythematosus_. Research seems to be ongoing, though not exploding in pace. A lot of the stuff one gets when searching is about engineered cell-penetrating antibodies, rather than natural ones.